Monitoring Plan and Strategy San Juan County Marine Resources Committee

Marine Stewardship Area Monitoring Plan and Strategy San Juan County Marine Resources Committee

DRAFT – June 27 2011

Marine Stewardship Area Monitoring Plan______

TABLE OF CONTENTS

Executive Summary

Part I. Draft MSA Prioritized Monitoring Strategy______

Section 1. Background 1.1 The San Juan County Marine Resources Committee and the Marine Stewardship Area 1.2 Targets of the MSA Plan 1.3 Threats Affecting Marine Biodiversity 1.4 Species and Groups of Concern 1.5 Database of Monitoring Efforts in the MSA 1.6 References to Ecosystems and Biological Communities 1.7 Recommendations of the MRC for Implementation of the Monitoring Program 1.8 Need for a Monitoring Strategy

Section 2. Development of a Prioritized Monitoring Strategy for the MSA 2.1 Coordination 2.2 Local Guidance 2.3 Structuring a Monitoring Strategy 1. Assessing Information Needs a. User Groups b. Use of Monitoring Information c. Key Questions 2. Identifying Gaps and Needs a. MSA Monitoring Plan b. Monitoring coordination process (May 2010 – June 2011) 3. Prioritizing Monitoring Efforts a. Focusing Monitoring Efforts b. Criteria for Ranking Monitoring Efforts 4. Supporting Effective Existing Monitoring Efforts a. Local Monitoring Groups b. All Other Monitoring 5. Establishing Monitoring Networks a. Coordination among Efforts b. Who Collects Monitoring Information c. Partnerships 6. Providing Access to Monitoring Information a. Infrastructure 7. Funding Support

2 a. Local b. Regional c. State d. Tribal e. Federal f. Trans-boundary

Section 3 A Prioritized Monitoring Strategy for the MSA 3.1 Next Steps for a 3 year Timeframe

Part II. Listing of local and ongoing monitoring in the MSA

Part III. Monitoring Plan for the MSA: Status, Research and History

Section 1. Introduction

Section 2. Ecosystem and Biological Resources 2.1 Overview 2.2 Species and Groups of Concern 2.3 Plankton (relevant MSA Target: Seabirds and Pacific Salmon) 2.4 Aquatic Vegetation 2.5 Intertidal Habitats and Biotic Communities 2.6 Subtidal Habitats and their Biota 2.7 Fish 2.8 Marine Birds 2.9 Marine Mammals

Section 3. Physical Environment and Habitat 3.1 Overview 3.2 Marine Waters (Temperature, Salinity, Density, Stratification, Dissolved Oxygen) 3.3 Circulation, Current Modeling Efforts 3.4 Intertidal and Coastal Monitoring

Section 4. Socio-cultural Targets 4.1 Overview 4.2 Targets

Section 5. Monitoring Threats to the MSA 5.1. Climate Change 5.2 Potential Sea Level Rise 5.3 Toxic Contamination 5.4 Oil Spills 5.5 Nutrients and Pathogens 5.6 Fresh Water Inputs to the Nearshore Zone 5.7 Desalinization Plant Outflows 5.8 Land Use 5.9 Overwater Structures 5.? Boat Traffic 5.? Non-Indigenous Species 5.? Harvest

3 Section 6. Summary of Monitoring Plan Recommendations 6.1 List of specific recommendations by MRC

Section 7. Monitoring, Implementation, and Adaptive Management 7.1 Overview 7.2 Draft Strategies/Benchmarks

FIGURES Figure 1 Salinity (2000-2004, JEMS) Figure 2 Dissolved Oxygen (2000-2004, JEMS) Figure 3 Temperature (2000-2004, JEMS) Figure 4 Temperature at Race Rocks Figure 5 Map of all Monitoring Programs Figure 6 Map of Monitoring Programs by Ending Date Figure 7 Map of Monitoring Programs by Organization Figure 8 Map of Monitoring Programs by Threat/ Target

TABLES

Table 1 Local and ongoing monitoring in the MSA Table 2 Top threats affecting all marine biodiversity targets in the MSA Table 3 Top stresses affecting the socio-cultural targets Table 4 Socio-cultural Targets Table 5 Chemicals of current concern in Puget Sound Table 6 Emerging contaminants of local concern Table 7 Anticipated emerging contaminants of local concern

APPENDICES

Appendix A Ranking Matrix (draft) Appendix B Criteria Lists Appendix C Potential Partners Appendix D Database of Existing Monitoring Programs in the MSA Appendix E Indicators and Key Attributes for Pacific Salmon (CAP Workbook) Appendix F References for Monitoring Strategy

4 Acknowledgements: The MSA Monitoring Plan was prepared for the San Juan County Marine Resources Committee by members of the MRC and MRC Science Subcommittee (2008-2011), with review by others:

MRC Members and Staff: Dr. Kenneth P. Sebens, Director UW FHL, UW Dept. of Biology, Chair, MRC Science Subcommittee (editor) Susan Key, MRC Monitoring Coordinator (editor) Dr. Richard Strathmann, UW FHL/UW Dept. of Biology Tina Whitman, Friends of the San Juans Gregg R. Dietzman, White Point Systems Inc. Barbara Rosenkotter, SRFB San Juan County Lead Entity Coordinator Mary Knackstedt, SJC Marine Resources Committee Coordinator Jody Kennedy, SJC Marine Resources Committee Coordinator Ed Hanson, SJC Marine Resources Committee Coordinator Dr. Barbara Bentley Jim Slocomb, Laura Arnold, David Loyd, Mary Masters, Michael Durland

Others: Phil Green, The Nature Conservancy Dr. Claudia Mills, UW FHL Kari Koski, The Whale Museum, Soundwatch Coordinator Dr. Terrie Klinger, UW FHL, UW SMA Dr. Donald Rothaus, Washington Department of Fish and Wildlife Eric Eisenhardt, Washington Department of Fish and Wildlife Dr. Jan Newton, UW APL, FHL Dr. Joe Gaydos, SeaDoc Society Dr. Kevin Britton Simmons, UW FHL Dr. Rich Osborne, The Whale Museum Rowann Tallmon, past coordinator, WSU Beach Watchers San Juan County Russel Barsh, Director, KWIAHT Dr. Gary Greene, Tombolo Institute and UW FHL Ed Hale, Stormwater Utility Steering Committee member, Utility Manager, SJC Public Works Shireene Hale, Senior Planner, SJC Community Development & Planning Jeff Hanson, San Juan Econet Coordinator Vicki Heater, Water Resource Management Committee, SJC Health & Community Services Dr. Carolyn Friedman, UW SAFS Dr. Robin Kodner, Beam Reach, UW Oceanography, UW FHL Dr. Tina Wyllie-Echeverria, Wyllie-Echeverria Associates Kirsten Evans, UW/Consultant Dr. Michael O’Donnell, UW FHL Dr. Jacques White, TNC Andrew van Eck, UW Biology, UW FHL April Phelps Ford, SJNI Dr. Jack Bell, UW FHL Dr. Jason Wood, The Whale Museum Dr. Thomas Mumford, WDNR Dr. Megan Dethier, UW FHL Dr. John K. Horne, UW SAFS Dr. Fiona Norris, Education Director, San Juan Nature Institute Brian Rader, Coordinator, SJC Pollution Prevention Program Barbara Rosenkotter, Lead Entity Coordinator, SJC Chapter for Salmon Recovery Tom Sage, PE, Stormwater Engineer, SJC Public Works Shann Weston, coordinator, WSU Beach Watchers San Juan County

5 Common Acronyms Used

CAO – Critical Areas Ordinance, WA State Growth Management Act FHL – University of Washington Friday Harbor Laboratories (UW FHL) FOSJ – Friends of the San Juans IND – Indicator JEMS – Joint Effort to Monitor the Strait KEA – Key ecological indicator MESA – Marine Ecosystem Analysis Puget Sound Project MRC – San Juan County, Marine Resources Committee NAGISA – National Geography in Shore Areas NGO – Non-Governmental Organization NIS – Non-indigenous Species NMFS – National Marine Fisheries Service NOAA – National Oceanic and Atmospheric Administration NWSC – Northwest Straits Commission PSAT – Puget Sound Action Team PSAMP – Puget Sound Ambient Monitoring Program PSNERP – Puget Sound Nearshore Ecosystem Restoration Project PSP – Puget Sound Partnership PSR – Puget Sound Region PSS – Puget Sound Science, PSP QAQC – quality assurance and quality control RCO – WA State Recreation and Conservation Office RITT – Puget Sound Recovery Implementation Technical Team SJC – San Juan County SJI – San Juan Initiative SMP – Shoreline Master Plan SRKW – Southern Resident Killer Whales TNC – The Nature Conservancy USFWS – U.S. Fish and Wildlife Service USGS – U.S. Geological Survey UW – University of Washington WDFW – Washington Department of Fish and Wildlife WDNR – Washington State Department of Natural Resources WDOE – Washington State Department of Ecology WRIA 2 – Water Resources Inventory Area number 2 (e.g. San Juan County)

TBA – to be added (sections still needed) XXX - missing citation, to be added

Marine Stewardship Area Monitoring Plan San Juan County Marine Resources Committee

Executive Summary:

The San Juan County Marine Resources Committee (MRC) is a citizen advisory committee appointed by the San Juan County Council. The MRC receives Federal Coastal Zone Management funding administered by the Washington Department of Ecology and by the Northwest Straits Commission. The San Juan Board of County Commissioners (now County Council) designated the waters of the entire County a Marine Stewardship Area in 2004 with the stated objective: “to facilitate the protection and preservation of our natural marine environment for the tribes and other historic users, current and future residents, and visitors”. With this resolution, the Marine Resources Committee (MRC) was charged with providing a formal study, with detailed recommendations for achieving this goal. The MRC thus began collecting and mapping available marine resources data to get a better picture of San Juan County’s marine life, and habitats, as well as potential measures that would help protect them. During 2004-2006, the MRC developed a plan for the Marine Stewardship Area, approved by the County Council in 2007, following the 5-S planning process developed by The Nature Conservancy.

Need for a Monitoring Plan. Despite the best efforts of the MRC to document the county’s marine resources, data do not exist to accurately assess the status or trends of the vast majority of the marine resources within the MSA. A particular shortcoming is that, frequently, data are only sufficient to describe the status of a particular species at one point in time and/or at one or very few sites. This attribute of existing data handicaps efforts to determine the current status of knowledge regarding species, habitats and communities and prevents an analysis of trends related to the threats from human activity and development. Moreover, the influence of environmental change resulting from the predicted shift in hemispheric and regional climate (e.g. warmer temperatures, wetter winters) on the range and distribution of native species, the spread of invasive species and of diseases may not be detected.

The first attempt to synthesize information and standardize a monitoring program occurred with the creation of CAO Best Available Science document (BAS 2008), produced by the CAO BAS Committee, with input from the MRC and other groups. This document and the MSA Monitoring Plan outline the need for additional descriptive information for marine species and the habitats in which they thrive, and advocate systematic monitoring of selected parameters designed to yield status and trend information for benthic and pelagic habitats. Without this program, valuable ecosystem services may not be protected, thereby jeopardizing the sustainability of the MSA.

7 Funding is always limited and yet a systematic and sustained monitoring program cannot rest solely on the volunteer labor or over-committed county staff. Fortunately, a number of monitoring programs already exist throughout the Puget Sound Region, detailed in the Puget Sound Ambient Monitoring Program (PSAMP Update, 2007, Puget Sound Science 2011) and other recent compilations. In some cases, these programs are adequate to evaluate impact to the MSA (e.g. spawning biomass of Pacific herring, adult salmon populations, pinto abalone abundance, and resident orca populations), and in other cases, while there may be a reasonably adequate regional monitoring program, data collection within San Juan County is not sufficient to evaluate impact within the county. In the latter case, it may not be sufficient to rely on federal or state programs to adequately monitor benthic and pelagic systems within the MSA. Rather, federal and state monitoring programs, augmented by a county sponsored program, will be needed. There are also situations where a resource is monitored within the MSA, but at only one or a few sites; locally funded programs can enhance ongoing monitoring in such cases. Finally, there will be many cases where species or groups of species found to be locally important fall outside existing monitoring programs, and our task will require designing a program for those, to adequately protect ecosystem health and biodiversity within the MSA.

Successful monitoring programs are designed to alert resource managers that protected resources are in jeopardy and to evaluate the effectiveness of protective measures. Within the MSA this design must take into account multiple natural and modified habitat types in benthic and pelagic regions. While the location of monitoring sites will depend on specific objectives (e.g. water quality assessment, population abundance and distribution, community structure, etc.) effort must be made to consider the MSA as a functioning sub-unit within larger regional jurisdictions with sampling occurring at a suitable frequency to compute status and trend estimates. Because this objective is broad in scope, partnering with federal, state and tribal resource management agencies, NGOs, and others is essential.

Targets of the MSA Plan are defined as those groups of species, and entire biotic communities, that are critical to conserve and protect ecosystem services and biodiversity within the MSA and which must be monitored to determine their current status and direction of change. Some targets are chosen because the distribution and density of these species or communities are poorly known but population stability is threatened by particular activities that are on the rise (e.g. bycatch associated with fish harvest, stormwater discharge over intertidal communities). Others are targets because the link between human activity and species decline has been established (e.g., recreational harvest of groundfish, impact of over-water structures on nearshore benthic plant survival and juvenile fish migration). The MSA Plan identifies the following targets:

- Rocky intertidal communities - Rocky subtidal communities - Nearshore sand, mud and gravel communities - Rockfish, lingcod and greenling - Seabirds - Marine mammals - Pacific Salmon, forage fish

For each of these targets, the MSA Plan also identifies key ecological attributes (KEAs), or indicators which are either species, groups of organisms, or chemical/physical processes which allow an assessment of ecosystem stability and biodiversity. The MSA Plan also sets out three socio-cultural targets involving human use of the marine environment and various species. They

8 are: enjoyment of the marine environment, support for marine-based livelihoods, and maintenance of Cultural traditions including ceremonial, subsistence, and spiritual uses and aspects.

Threats Affecting Marine Biodiversity. In addition to targets noted above, the MSA plan also identified and defined sixteen threats affecting marine biodiversity targets within the MSA (Table 2, MSA 2007). These threats must also be monitored to determine their persistence and importance, to document the trajectory of influence and evaluate the effectiveness of regulations designed to protect ecosystem services and biodiversity.

Ecosystems and Biological Resources. As part of the process of designing a monitoring program, we sought input from members of the Marine Resources Committee Science Subcommittee. Each member was tasked with compiling a list of elements they deemed integral to a monitoring program in their area of expertise. To augment and enrich this effort, we also interviewed a select group of regional scientists and resource managers using a structured interview format. Many of the species, habitats and ecosystem components discussed here have also been covered in the San Juan County MSA Plan (2007) and the San Juan County Best Available Science for Critical Areas document (2007). For the broader Puget Sound Region, the 2007 Puget Sound Update (PSAT 2007) and Puget Sound Science (PSP) web-based status reports, PSS 2011) are extremely informative. These documents contain excellent maps of biological resources, habitats, protected areas and other data relevant to this monitoring program. This document will not try to duplicate all the information provided in the BAS document, but will be limited to discussion of existing monitoring programs, and recommendations for future monitoring. Background information, existing status, and information from other regions will be brought in as needed. Species and Groups of Concern. The MSA includes species considered endangered or threatened, as well as species whose populations have declined significantly over the past century or over recent decades. While we are concerned with the biodiversity of the MSA overall, we will also pay particular attention to species whose populations are in danger within the MSA or within the broader region. Example species include orcas, abalone, native oysters, eelgrass, rockfish, and Chinook salmon. Species and groups of concern are also set out as targets in Table 1 of the MSA Plan (2007). For the larger region, PSAMP (2007, Table 2-1) lists 63 species of concern in Puget Sound (Gaydos 2004), defining them as those species that “require special initiatives to ensure protection and survival of their populations”. Of these, three were invertebrates, 27 were fishes, 23 were birds, nine were mammals and one was a reptile. Fourteen of these species are defined as threatened or endangered by the federal government or by the state. Most, if not all, of these are species of concern for the SJC MSA as well.

Database of Monitoring Efforts in the MSA. An important part of this exercise was the identification and listing of all monitoring programs, regardless of status, that have occurred or are occurring in San Juan County. In Appendix D, we list, in database format, all existing programs being conducted by federal, tribal, state and county governments and NGOs such as Friends of the San Juans and The Nature Conservancy (certain programs that have been terminated are also listed. We strongly suggest that future monitoring of MSA targets include the continuation of ongoing programs (Table 1) as well as the selective resumption of programs that have been terminated.

Recommendations of the MRC for Implementation of the Monitoring Program:

1. Establish current status and detect changes over time and the level of threat for: specific toxic chemicals and nutrients in coastal water, streams, stormwater and wastewater outflow areas, discharges from desalinization plants, contaminants present in intertidal and subtidal sediments (baseline for oil spills), and also for physical modification of shorelines, and increased sediment loading from construction.

2. Establish current status and detect changes in health over time for: rocky intertidal and subtidal communities and their component species (e.g. sea urchins, sea cucumbers, kelp), and soft sediment intertidal and subtidal communities and their component species (e.g. clams, worms, sand lance). This monitoring is not currently being conducted by state or federal agencies, and should include the presence of nonindigenous (invasive, exotic) species, overall biodiversity, changes in trophic structure (food webs), and response to environmental change (e.g. ocean warming, acidification).

3. Determine groundfish population health and viability by partnering with state agencies that are monitoring groundfish in mandatory (WDFW) as well as voluntary no-take (and comparison) areas established by the county, eelgrass in embayments and near/under over-water structures within the MSA, forage fish in nearshore habitats, juvenile salmon in nearshore habitats, salmonids in streams, and marine mammals in local habitats (including interactions with humans). Additional local monitoring will be needed here.

4. Determine environmental change and level of threats by partnering with state agencies to expand the number of sites that are being monitored for physical, chemical and biological characteristics of the water column (e.g. JEMS), also using local monitoring efforts.

5. Determine population health and viability using monitoring conducted by federal and state agencies – orcas (killer whales), abalone, adult salmon, forage fish in offshore habitats, floating kelp beds, many marine and coastal birds, and groundfish in marine preserves and certain non-preserve areas (probably without additional monitoring locally)

6. Sociocultural targets must be monitored locally to determine how MSA protection is affecting local stakeholders. These include: enjoyment of the marine environment, support for marine-based livelihoods and maintenance of cultural traditions including ceremonial, subsistence, and spiritual uses and aspects.

Local Guidance for the Prioritized Monitoring Strategy. The MRC’s monitoring subcommittee gave clear direction to focus prioritization efforts on the proposed monitoring elements called out in the Marine Stewardship Area Monitoring Plan, and to link prioritization to the implementation of the overall MSA Plan’s targets, benchmarks, strategies and threats. In addition, the coordinator conducted interviews with a cross section of those involved in monitoring and those who use the results. The following basic guidance statements have floated to the top across the spectrum.

10 • Use the San Juan Islands Marine Stewardship Area as a sub-unit. • Build on what has and/or is occurring in the local monitoring arena, and “add value” to these programs. • Incorporate “terrestrial” monitoring efforts, especially the impacts of managing runoff. It is a “short run to the sea” in the Islands, and what people do on the land impacts key nearshore and marine areas. • Monitoring needs to “tell a story” about the health of our Islands ecosystem, and to lead to behavior change; to link personal choices, property management, and land use decisions to ecosystem health and the ecosystem services that support us (soil, water, vegetation, wildlife). • Community participation is vitally important. People collecting data develop an understanding of our ecosystem, and of how their choices impact ecosystem health. Friends and neighbors talk to each other about what is going on and how to make it better. • Support needs to go to monitoring that addresses local issues, that indicates what is happening locally, and that provides guidance to those who live and work here. • Find the money to support a locally prioritized monitoring effort with a strong community volunteer component. Partnerships stand a better chance of getting funded.

Part I

Marine Stewardship Area Prioritized Monitoring Strategy

Section 1. Background

1.1 The San Juan County Marine Resources Committee and the Marine Stewardship Area. Formed in 1996, the Marine Resources Committee (MRC) is a volunteer citizen advisory committee appointed by the San Juan County Council. The San Juan Board of County Commissioners (now County Council) designated the waters of the entire county a Marine Stewardship Area in 2004 with the stated objective: “to facilitate the protection and preservation of our natural marine environment for the tribes and other historic users, current and future residents, and visitors.” With this resolution, the Marine Resources Committee was charged with providing a formal study with detailed recommendations for achieving this goal. The MRC thus began collecting and mapping available marine resources data to get a better picture of San Juan County’s marine life and habitats, as well as potential measures that would help protect them.

During 2004-2006, the MRC developed a plan for the Marine Stewardship Area (MSA), following the 5-S planning process developed by The Nature Conservancy. This plan outlined the need for additional descriptive information for marine species and their habitats, and advocated systematic monitoring of selected parameters designed to yield status and trend information. Without this program, valuable ecosystem services may not be protected, thereby jeopardizing the sustainability of the MSA. The MRC science sub-committee completed a draft MSA Monitoring Plan December 2009 linking MSA Plan benchmarks, threats, target areas, and species and groups of concern. A database of all monitoring efforts in the MSA was also compiled at that time (updated June 2011), and resources relevant to local ecosystems and biological communities were referenced.

1.2 Targets of the MSA Plan. Defined as those groups of species and entire biotic communities that are critical to conserve and protect ecosystem services and biodiversity within the MSA, and which must be monitored to determine their current status and direction of change.

12 Some targets are chosen because the distribution and density of these species or communities are poorly known but population stability is threatened by particular activities that are on the rise (e.g. by-catch associated with fish harvest, stormwater discharge over intertidal communities). Others are targets because the link between human activity and species decline has been established (e.g., recreational harvest of groundfish, impact of over-water structures on nearshore benthic plant survival and juvenile fish migration). The MSA Plan identifies the following targets: • Rocky intertidal communities • Rocky subtidal communities • Nearshore sand, mud and gravel communities • Rockfish, lingcod and greenling • Seabirds • Marine mammals • Pacific Salmon, forage fish

For each of these targets, the MSA Plan also identifies key ecological attributes (KEAs) linked with indicators, both of which are either species, groups of organisms, or chemical/physical processes which allow an assessment of ecosystem stability and biodiversity. Such species can be chosen because they are (1) charismatic, (2) commercially important, (3) rare and at risk of local extirpation or extinction, (4) respond negatively to environmental stress or perturbation, or (5) abundant and characterize the habitat or community. Expanding a monitoring program to include other species may be appropriate because results of ongoing research identify these species as important indicators of ecosystem change (e.g. use of lichen communities to monitor air quality).

1.3 Threats Affecting Marine Biodiversity. In addition to targets noted above, the MSA plan also identifies and defines sixteen threats affecting marine biodiversity targets within the MSA (Table 2, MSA 2007). These threats must also be monitored to determine their persistence and importance, to document the trajectory of influence and evaluate the effectiveness of regulations designed to protect ecosystem services and biodiversity.

1.4 Species and Groups of Concern. The MSA includes species considered endangered or threatened, as well as species whose populations have declined significantly over the past century or over recent decades. While we are concerned with the overall biodiversity of the MSA, we will also pay particular attention to species whose populations are in danger within the MSA or within the broader region. Example species include abalone, Chinook salmon eelgrass, native oysters, resident orcas, and rockfish. Species and groups of concern are also set out as targets in Table 1 of the MSA Plan (2007). For the larger region, PSAMP (2007, Table 2-1) lists 63 species of concern in Puget Sound (Gaydos 2004), defining them as those species that “require special initiatives to ensure protection and survival of their populations.” Of these, three were invertebrates, 27 were fishes, 23 were birds, nine were mammals and one was a reptile. Fourteen of these species are defined as threatened or endangered by the federal government or by the state. Most, if not all, of these are species of concern for the SJC Marine Stewardship Area as well.

Effective monitoring determines which species indicate population stability and biodiversity, are easy to identify, and are representative of larger groups. Some monitoring protocols combine rapid field assessment and substantial taxonomic lumping, with extensive collections that can provide accurate species identification at a later date if needed (e.g. NAGISA, http://www.coml.org/descrip/nagisa.htm).

Successful monitoring programs are designed to alert resource managers that key ecosystem functions (air, water, soil, vegetation, wildlife and habitats) are in jeopardy, and to evaluate the effectiveness of protective measures. While the location of monitoring sites will depend on specific objectives (e.g. water quality assessment, population abundance and distribution, community structure, etc.), note the following:

Recommendations • Consider the MSA as a functioning sub-unit within larger regional jurisdictions. • Sample at suitable frequencies to compute status and trend estimates. •   

1.5 Database of Monitoring Efforts in the MSA. Appendix D of the MSA Monitoring Plan lists all existing programs being conducted by local, state, regional, tribal, federal, and trans- boundary organizations in a database format known as the MRC Monitoring Database. The complete Database also lists programs that have been terminated.

Recommendation • We strongly suggest that the future monitoring of the MSA targets must include the continuation of ongoing programs as well as the selective resumption of programs that have been terminated.

1.6 References to Ecosystems and Biological Communities. Many of the species, habitats and ecosystem components discussed in the MSA Monitoring Plan have also been covered in the San Juan County MSA Plan (2007) and the San Juan County Best Available Science for Critical Areas document (2007). For the broader Puget Sound Region, the 2007 Puget Sound Update (PSAT 2007) and Puget Sound Science (PSP) web-based status reports, PSS 2011) are extremely informative. These three documents contain excellent maps of biological resources, habitats, protected areas and other data relevant to the MSA monitoring program.

Fortunately, a number of monitoring programs already exist throughout the Puget Sound Region, detailed in the Puget Sound Ambient Monitoring Program (PSAMP Update, 2007) and other recent compilations. In some cases, these programs are adequate to evaluate impact to the MSA (e.g. spawning biomass of Pacific herring, adult salmon populations, pinto abalone abundance, and resident orca populations), and in other cases, while there is a reasonably adequate regional monitoring program, data collection within San Juan County is not sufficient to evaluate impact within the county. There are also situations where a resource is monitored

14 within the MSA, but at only one or a few sites; local ‘place based’ programs can enhance ongoing population monitoring. Finally, there will be many cases where species or groups of species, found to be locally important fall outside existing monitoring programs, and our task will require designing a program to adequately protect ecosystem health and biodiversity within the MSA. In each of these cases, we make the following recommendation.

Recommendation • Regional, state, tribal, federal and trans-boundary organizations that are involved in monitoring efforts in the San Juan Islands, or that require monitoring within San Juan county, contribute funding to support locally based programs that will augment these monitoring efforts.

1.7 Recommendations of the MRC for Implementation of the Monitoring Program.

5. Determine population health and viability using monitoring conducted by federal and state agencies – orcas (killer whales), abalone, adult salmon, forage fish in offshore habitats, floating kelp beds, many marine and coastal birds, and groundfish in marine preserves and certain non- preserve areas (probably without additional monitoring locally)

6. Sociocultural targets must be monitored locally to determine how MSA protection is affecting local stakeholders. These include: enjoyment of the marine environment, support for

15 marine-based livelihoods and maintenance of cultural traditions including ceremonial, subsistence, and spiritual uses and aspects.

1.8 Need for a Monitoring Strategy. Managers and researchers are challenged in that a biological community contains hundreds to thousands of species, and it is not possible or desirable to monitor all species present. Consequently, well-defined criteria must be established to direct sampling from which spatial and temporal generalizations can be made. Management of marine resources is increasingly viewed from an ecosystem perspective (ecosystem-based management), recognizing that single species management is not sufficient to detect ecosystem changes or to identify potential impacts of human activity. The objective of biodiversity monitoring is to determine species composition and relative abundance within a specified area, community, or habitat. Ideally, we would like to have data for all species present, but that is rarely possible, therefore

• a strategy to focus monitoring efforts is crucial.

Despite the best efforts of the MRC to document the county’s marine resources, data do not exist to accurately assess the status or trends of priority species and key areas, much less all of the marine resources within the MSA. Frequently, data are only sufficient to describe the status of a particular species at one point in time and/or at one or very few sites. This handicaps efforts to determine the current status of knowledge regarding species, habitats and communities, and prevents an analysis of trends related to the threats from mismanaged human activity and development. Moreover, the influence of environmental change resulting from the predicted shift in hemispheric and regional climate (e.g. warmer temperatures, wetter winters) on the range and distribution of native species, and the spread of invasive species and diseases may not be detected. Therefore

• prioritizing to fill known data gaps and needs is also crucial.

The MRC is working with the University of Washington Friday Harbor Labs (FHL), marine and terrestrial resource managers, and other partners to develop a monitoring strategy to help assess and track the condition of habitats and species indicative of ecosystem health. We need a program that

• tracks biodiversity and assesses ecosystem health • measures the effectiveness of the MSA strategies and • supports adaptive management of local natural resources.

This program needs to incorporate, streamline and coordinate the monitoring efforts called out in the following local planning processes (see Appendix B, Criteria Lists, Relevant Plans):

Marine Stewardship Area Management Plan and MSA Monitoring Plan San Juan Chapter (WRIA 2) of the Puget Sound Chinook Salmon Recovery Plan Shoreline Master Plan updates (San Juan County; Town of Friday Harbor)

16 SJC Action Agenda (Puget Sound Action Plan); local Implementation Committee efforts SJC Critical Areas Ordinance update SJC Land Bank Habitat Conservation Plan Stormwater Monitoring Plan Watershed Management Action Plan & Characterization Report (WRIA 2)

Section 2. Development of a Prioritized Monitoring Strategy for the MSA

2.1 Coordination. In order to move monitoring efforts forward, the MRC contracted a part time monitoring coordinator May 17, 2010 through June 2011. On behalf of the MRC’s monitoring and science sub-committees, the coordinator issued invitations to those involved in local monitoring efforts to join this process. The coordinator contacted these key individuals involved in monitoring efforts, or who use data, or who are involved in outreach and education plus select MRC members to form a Monitoring Group. Monitoring Group meetings were held throughout 2010 and 2011, and the coordinator conducted interviews with key people involved in monitoring in the Islands (for a list, see p. 5). The MRC held community monitoring roundtables on each of the major islands (Lopez, Orcas and San Juan) during the fall of 2010. Results from the interviews, meetings and community roundtables provided input for the initial draft and for the revision of this strategy. In addition, the coordinator reviewed the planning documents listed in Appendix F, References.

A draft Prioritized Monitoring Strategy for the MSA was submitted to the Northwest Straits Commission June 11, 2010, and a revised Strategy plus a SUMMARY of Local Monitoring Efforts were submitted June 2011. The strategy and summary are most importantly tools for adaptive management, and are therefore designed to be living processes (more of a verb than documents) that are updated annually by the MRC (Strategy) and continually by monitoring groups via the web (Summary). Partnerships and feedback loops are essential, as is communication between data collectors and data users.

This strategy is the beginning of a comprehensive effort to prioritize and coordinate monitoring that is linked to the implementation of the Marine Stewardship Area Plan. However, there is far more monitoring needed than can be accomplished with current resource levels. Therefore, an effort has been made to develop a 3 year timeline with action items and next steps associated with 2011/2012, 2012/2013, and 2013/2014. These priorities are reflected in Section 3, Next Steps for a 3-Year Timeframe.

2.2 Local Guidance for the Prioritized Monitoring Strategy. The MRC’s monitoring subcommittee gave clear direction to focus prioritization efforts on the proposed monitoring elements called out in the Marine Stewardship Area Monitoring Plan, and to link prioritization to the implementation of the overall MSA Plan’s targets, benchmarks, strategies and threats. In addition, the coordinator conducted interviews with a cross section of those involved in monitoring and those who use the results. The following basic guidance statements have floated to the top across the spectrum.

17 • Build on what has and/or is occurring in the local monitoring arena, and “add value” to these programs. • Incorporate “terrestrial” monitoring efforts, especially the impacts of managing runoff. It is a “short run to the sea” in the Islands, and what people do on the land impacts key nearshore and marine areas. • Monitoring needs to “tell a story” about the health of our Islands ecosystem, and to lead to behavior change; to link personal choices, property management, and land use decisions to ecosystem health and the ecosystem services that support us (soil, water, vegetation, wildlife). • Community participation is vitally important. People collecting data develop an understanding of our ecosystem, and of how their choices impact ecosystem health. Friends and neighbors talk to each other about what is going on and how to make it better. • Support needs to go to monitoring that addresses local issues, that indicates what is happening locally, and that provides guidance to those who live and work here. • Find the money to support a locally prioritized monitoring effort with a strong community volunteer component. Partnerships stand a better chance of getting funded.

2.3 Structuring a Monitoring Strategy. Building an effective monitoring program that generates meaningful information and contributes to adaptive management requires a process that incorporates the following seven aspects: assessing who needs the information and how it is used with feedback loops between all users, and identifying key questions that address local issues; identifying gaps and needs; prioritizing monitoring efforts; supporting effective existing monitoring efforts; establishing networks, partnerships and feedback loops at all levels; providing access to monitoring information; and finding funding sources.

1. Assessing Information Needs Who uses the information (user groups) generated by monitoring and how it is used helps shape the design of monitoring programs. Key questions that address current local issues can also shape the design of monitoring programs. Recommendations • Establish a process to continually update monitoring needs and data gaps • Establish feedback loops between all user groups that support adaptive management a. User Groups – the following is a partial list of who currently uses information generated by monitoring efforts. 1) Resource managers (SJC) – water resources management, salmon recovery, 2) Program managers (SJC) – pollution prevention, environmental health, Land Bank, stormwater utility, Conservation District farm and forest planning staff 3) Local elected decision makers – county council members, Town of Friday Harbor council members and mayor, neighborhood associations 4) Advisory boards (SJC) – Marine Resources Committee, Stormwater Advisory Committee, Agricultural Resources Council, Economic Development Council 5) NGO’s – Friends of the San Juans, Kwiaht, San Juan Nature Institute, San Juan Preservation Trust 6) Other – WSU Beach Watchers, Stewardship Network

18 7) Researchers, academic institutions and programs 8) Regional, state, tribal, federal and trans-boundary entities b. Use of Monitoring Information – the following are examples of how monitoring information is used locally. 1) Program direction – Beach Watcher participation, focus for the SJC Pollution Prevention program, where to install stormwater infrastructure (rain gardens, wetland restoration, conveyance and infiltration systems), restoration projects, set local thresholds for non-point source pollutants and identify problem areas, track volumes of water being put to beneficial uses, conservation land acquisition. 2) Local land use and policy decisions, changes in local laws and codes. 3) Landowners and businesses - introduction or continuation of best management practices with regard to soil, water, stormwater, vegetation, wildlife; pollution prevention; guidance for property owners to maximize groundwater recharge with stormwater BMPs. 4) Outreach and education – translation of monitoring information into understandable language for the public in order to inform product and/or behavior choices pertaining to homes, gardens, barns, businesses, property management, and vehicle maintenance. 5) Enforcement – to prevent or trigger enforcement actions.

c. Key Questions – to be effective, data resulting from monitoring needs to be used. Following are important questions that monitoring programs can help answer at the local level. 1) What are the impacts of single family residences on the ecosystem health of nearby shorelines, wetlands, groundwater recharge areas, stream courses, and wildlife habitat? 2) What are the impacts of stormwater from urban growth areas on ecosystem health? 3) Which BMPs (best management practices) are working, and which are not? 4) Where are key habitat areas (forage fish beaches, eelgrass beds, shellfish beds, estuaries, feeder bluffs, wetlands, stream courses, etc.) and how are these areas being impacted? 5) How do threatened and endangered species use the Island ecosystem? 6) Are we maintaining appropriate habitat for the recovery of endangered or threatened species? 7) How do identified threats and stressors impact habitat function? 8) We want to protect what we have, but we don’t know what we have. The question “what do we have?” underscores the need for establishing and monitoring baselines in key areas (MSA target areas and marine reserves, at a minimum).

2. Identifying Gaps and Needs – what additional data is needed to address local issues and contribute to adaptive management? a. The MSA Monitoring Plan proposed the following and contains additional information pertinent to each.

19 1) Plankton – continue the Pelagic Ecosystems monitoring (Research Apprenticeship, UW FHL) through the year and expand the number of sites visited from 2-3 to 5-10. 2) Aquatic Vegetation (seagrasses, kelp, and other marine algae) – in addition to monitoring stem density, characterize population sub-structuring and site-specific clonal diversity patterns to understand the impact of natural and anthropogenic disturbance events on the health and resilience of seagrass flora. 3) Salt Marshes – map and monitor using aerial photography plus extensive groundtruthing. 4) Rocky Intertidal Communities - maintain the UW FHL rocky intertidal sampling at Reuben Tarte, Cattle Point and Cantilever Point sites. Add sites at Cedar Rock and Pt. George on Shaw Island, and Argyle Lagoon and False Bay on San Juan Island. SJC could partner with FHL and the NPS to establish or maintain sites at American Camp and English Camp. Establish new intertidal monitoring sites on all the major islands, including rocky shores and soft sediment beaches or mudflats. 5) Soft Substrate Subtidal Communities (nearshore sand, mud and gravel) - maintain the UW FHL sampling at Pt. Caution/Collins Cove sites. Add sites at Cedar Rock and Pt. George on Shaw Island, and near Argyle Lagoon and outside False Bay on San Juan Island. Establish subtidal monitoring sites at rocky shores and soft sediment habitats of all major islands, especially outside protected marine areas where monitoring sites don’t currently exist. Complete a broad-scale survey and basemap of subtidal habitats within the MSA to establish species presence and map habitat types in conjunction with other monitoring efforts such as mapping rockfish habitat. 6) Rockfish, Lingcod and Greenling – broaden the range of sites and continue assessments of abundance and length distribution in regulatory, voluntary and open areas on a regular basis to test hypotheses about the efficacy of harvest controls. Conduct a one-time assessment of all suitable rockfish habitat in the San Juans. 7) Surf Smelt and Pacific Sand Lance – periodic monitoring (every 5 years?) of documented spawning sites, and exploratory surveys of potential spawn habitat. Assess larval and adult distribution and abundance. 8) Pacific Herring – annual spawning site surveys of documented sites and additional surveys of potential sites. 9) Marine Birds – conduct surveys every three to five years using protocols developed by MESA and WDFW for PSAMP. Yearly monitoring of black oystercatchers and pelagic cormorants, which are indicator species as identified by the Marine Stewardship Area Plan. 10) Desalinization Plant Outflows – field monitoring including impacts of effluent on fish movement and sampling of effluent water to be tested for salinity, chlorine and copper at the minimum. 11) Sediments – collect and archive frozen sediment samples to document hydrocarbons and other contaminants prior to an oil spill or other contamination. 12) Oil Spills – see Sediments above.

20 13) Shoreline Vegetation – use existing vertical and oblique aerial photo data sets for different time periods to monitor change over time in shoreline vegetation type, cover and overhang. 14) Docks, Marinas and Other Structures – a retrospective survey of existing docks, with data on distribution and abundance of eelgrass or other selected organisms under and at distances from docks; data on dock age, size, design and orientation; data on water depth; data on boats and boat use via interviews. 15) Non-Indigenous Species (NIS) – determine the spread of established NIS via field sampling and/or aerial photo analysis where possible.

b. In addition, the following are gaps that were identified during 2010 and 2012 through Monitoring Group meetings, the interview process, and Community Monitoring Roundtables. 16) More spatially diverse data on local precipitation inputs to accompany water quality and water quantity monitoring. 17) Add details from the adaptive management and monitoring plan that is currently being developed by the WRIA2 Lead Entity for Salmon Recovery, Salmon Recovery staff from the Puget Sound Partnership, and the Puget Sound Recovery Implementation Technical Team (RITT). 18) An accepted process of setting and reviewing quality assurance and quality control (QAQC). 19) Funding to maintain volunteer coordination at current levels and increase volunteer coordination to the levels needed to carry out prioritized monitoring efforts. 20) Coordination and information sharing among these efforts and with monitoring at all levels. 21) Incorporation of monitoring results into the MSA Monitoring Plan, into local land use decisions, and into the implementation of other local plans.

3. Prioritizing Monitoring Efforts There are limited resources (time, people, funding) available for monitoring. How do we prioritize monitoring efforts at the local level and tailor monitoring programs for best results? a. Focusing Monitoring Efforts – certain “screening questions” may need to be answered before a monitoring effort goes through a more detailed ranking process. Following are questions that can effectively guide the design and prioritization of monitoring programs. 1) Is the monitoring effort sustainable (infrastructure, personnel, funding) over the long term? 2) Does the monitoring effort inform and steer forward current local planning efforts? See Appendix B, Criteria, Relevant Plans. 3) Does the monitoring program focus on early indicators of success, or failure? 4) Is this monitoring effort sequenced in the “right order?” Certain monitoring data may need to be collected before the next step in a monitoring plan. 5) Is there current funding available? Can this funding be leveraged? Is there potential funding coming down the pike?

21 6) Does the QAQC level (collection by K-12 students, community volunteers, college students, graduate students, PhD students, or professionals) match the use the data will be put to (outreach, decisions made by elected officials or program managers, enforcement)?

b. Criteria for Ranking Monitoring Efforts – there are an infinite number of variables to monitor, and limited money, time and people to do so. Developing a ranking process is one way to prioritize local monitoring efforts. This process provides a feedback loop between participants, gives direction to local efforts, and demonstrates that there is an effort to coordinate monitoring at the local level. Appendix A shows a draft monitoring matrix with the following criteria that has been developed collaboratively as a first step in local prioritization. The weighting of the criteria has yet to be developed. Appendix B lists elements of various criteria. 1) Required Monitoring - Is the monitoring project required of San Juan County, or within San Juan County, and if so, by which agency? See Appendix B. 2) Program Direction - Will the monitoring program inform local program managers or coordinators? See section 2.3.1.b. above, Use of Monitoring Information. 3) Outreach Impact – Indicate the level of public interest, awareness, and involvement. Will results help support behavioral change? 4) Protection Effort and/or Restoration Project – Is the monitoring project associated with a protection effort/s and/or restoration project/s? 5) Enforcement Component - Will results of the monitoring effort prevent (by providing information leading to behavior change) or trigger an enforcement action? If triggered, which agency will conduct the enforcement action? See Appendix B. 6) Relevant Plans - Is the monitoring program called for in current planning efforts, and if so by which plan? Specify “benchmarks” if appropriate. See Appendix B. 7) Priority Area &/or Target - Does the monitoring effort focus on a priority area/s or target/s that are called out in planning efforts? See Appendix B. 8) Beneficial Use - Does the monitoring effort focus on a beneficial use (as defined in WAC 173) related to water quality and quantity in marine and/or surface waters? See Appendix B. 9) Threats/Stressors - Does the monitoring effort focus on a threat/s that is/are called out in planning efforts? See Appendix B. 10) Baseline – Is the monitoring project establishing and/or tracking a baseline? 11) Estimated Cost – Include a cost range; this criterion may not be weighted. 12) Funding Status – Is the project currently funded? If so, how and how much? 13) Partners – Indicate actual and potential partners.

4. Supporting Effective Existing Monitoring Efforts Monitoring efforts that are currently ongoing, and efforts that have ceased solely due to lack of funding may contain components that fit into the more comprehensive MSA Monitoring Plan. This plan “strongly suggests that future monitoring of MSA targets include the continuation of ongoing programs as well as the selective resumption of programs that have been terminated.” See Table 1, a three page SUMMARY of Local Monitoring Efforts compiled in spring of 2011.

22 a. Local Monitoring Groups – those organizations with a local base that are or recently have been conducting monitoring throughout San Juan County or at specific locations within the county noted by parentheses. • Beam Reach – audio output of vessels; phytoplankton (including toxic varieties) • The Center for Whale Research – Southern Resident Killer Whale annual census • Fisherman Bay Marine Health Observatory (Lopez) – multiple marine, nearshore, freshwater and terrestrial projects • Friday Harbor Labs (UW) – multiple marine habitat and species assessments • Friday Harbor Marine Health Observatory (MHO) – multiple marine, nearshore, freshwater and terrestrial projects • Friends of the San Juans – project specific • Indian Island Marine Health Observatory (Orcas Island) - multiple marine, nearshore, freshwater and terrestrial projects • Lopez Community Salmon Team - multiple marine, nearshore, freshwater and terrestrial projects • Mike Kaill Port of Friday Harbor aquarium (San Juan Island) – aquarium water quality • Kwiaht – multiple marine, nearshore, freshwater and terrestrial projects • SJC Environmental Health Department – groundwater, septic systems • SJC Land Bank – multiple terrestrial projects • SJC Public Works - stormwater • SeaDoc Society – multiple marine projects • SJC Environmental Health Department – groundwater, septic systems • SJC Land Bank – multiple terrestrial projects • SJC Public Works – stormwater • San Juan Nature Institute – multiple marine and terrestrial projects with schools • San Juan Preservation Trust – multiple terrestrial projects • Town of Friday Harbor – Trout Lake watershed and system water consumption • Waldron Community Science (Waldron Island) - multiple marine, nearshore, freshwater and terrestrial projects • Water Systems and Municipalities on all islands • The Whale Museum (Soundwatch) - – Southern Resident Killer Whale and transient habitat use and behavior; vessel trends and compliance • WSU Beach Watchers – providing training and coordination for volunteers who participate in many of the above countywide monitoring efforts

b. All Other Monitoring Efforts - Appendix D of the MSA Monitoring Plan lists all existing programs being conducted by local, regional, state, tribal, federal and trans- boundary entities in a database format known as the MRC Monitoring Database. The complete database also lists programs that have been terminated.

5. Establishing Monitoring Networks There are myriad ways to monitor an infinity of details, and disparate groups have been conducting monitoring often without effective coordination. The result can be unproductive overlap and information that doesn’t mesh into the larger picture. In

23 addition, community volunteers are essential to accomplish needed data collection. As people are trained and participate in monitoring, they also gain knowledge about our local ecosystem and the results of personal and land use decisions on ecosystem health. Creating feedback loops and establishing monitoring networks at all levels with strong volunteer components will lead to more effective adaptive management and to a more informed public.

a. Coordination – How can we maximize our collective efforts so limited resources stretch further, and results are compatible at all levels? Coordination between local efforts and with monitoring conducted at the regional, state, tribal, federal and trans-boundary levels is necessary. Asking the following questions on an annual basis is a start. 1) What monitoring is currently occurring in the San Juan Islands and what has occurred? Use MRC’s Monitoring Database (Appendix 1, MSA Monitoring Plan, 2011), the CAO Best Available Science document (BAS 2008), and the Puget Sound Ambient Monitoring Program (PSAMP Update, 2007) as starting points. 2) What monitoring, assessment, and adaptive management tools are available at the regional, state tribal, federal and transboundary levels that can be utilized locally? 3) What additional species, biological communities, threats, and/or physical and chemical characteristics are being or will be monitored at other levels? 4) Which of the above also need monitoring at the local level?

b. Who Collects Monitoring Information – the level of training and QAQC can vary depending upon the intended use of monitoring information. Those collecting data can generally be divided into the following groups. 1) K-12 Students – currently trained and coordinated by Friday Harbor Labs (UW), Kwiaht, and San Juan Nature Institute. 2) Community Volunteers – currently trained and coordinated by Kwiaht, The Whale Museum, and WSU Beach Watchers 3) College and University – degree programs involving undergrads, graduates, PhDs 4) Professional – may be necessary if an enforcement element is involved

c. Partnerships – collaboration at the local, regional, state, tribal, federal and trans- boundary levels will maximize limited resources and reduce redundancy. Appendix C lists actual and potential partners. Feedback loops, coordination and strong partnerships between all partners are essential.

6. Providing Access to Monitoring Information Both those who conduct monitoring and those who use the results must have easy access to all monitoring information. They also must have a way to communicate their needs and results in a feedback loop that supports adaptive management. Monitoring data and the analysis or summary thereof often needs to be “translated” for the lay public, and for elected decision makers. Without a functioning infrastructure, monitoring information remains scattered, often does not reach those who need it most, and may be misinterpreted.

24 a. Infrastructure – what is needed in order for monitoring data to be effectively preserved, accessed and used? 1) A stable, well maintained and easily accessible monitoring data library/archive. 2) Analysis and synthesis of existing monitoring information related to local ecosystem functions and land use impacts. Translation of this information for the lay public and elected officials. Graduate and PhD students could assist on an ongoing basis, however overall coordination is needed. 3) Updates of key websites with a summary of monitoring results and links to relevant monitoring data and programs. Graduate and PhD students could assist on an ongoing basis, however overall coordination is needed. 4) Feedback loops between those conducting the monitoring (the data “producers”) and those using the results (the information “consumers”).

7. Funding Support Without funding support, true monitoring will not occur as monitoring inherently requires long term commitments of resources. Yet monitoring is essential to determine how we are impacting ecosystem health and services – what we are doing wrong, and most importantly, what we are doing right. State and federal grant programs need to incorporate monitoring components. Making the most of funding dollars necessitates coordination and collaboration at all levels, feedback loops, and a healthy community volunteer component. Communities will support monitoring efforts when the information that is generated is seen as useful, i.e. “when I make this choice, I am improving the quality of the water that I drink.”

See Part II for a complete listing of actual or potential funders for locally based monitoring efforts, current as of June 2011.

Section 3. Prioritized Monitoring Strategy for the MSA

3.1 Next Steps for a 3 Year Timeframe. How can we, at the local level, move monitoring forward so that adaptive management actually occurs? Following are collaboratively identified next steps to be undertaken over the next three years, many of which are or need to be occurring on a continuing basis. Note that the monitoring coordinator position will be unfunded as of June 2011. The Monitoring Group consists of members of the MRC’s monitoring and science subcommittees, with additional members involved in actual data collection, terrestrial monitoring efforts, local resource management, and outreach and education. Next steps that require group effort and process are indicated by (Group). Next steps that can be accomplished by a coordinator are indicated by (Coordinator). Next steps that could be accomplished by a graduate student assisting a coordinator are indicated by (Coordinator and Grad Student). Next steps that need work by both a coordinator and the group are indicated by (Coordinator and Group) Next steps that can be accomplished by the SJC Marine Resources Committee are indicated by (MRC and Coordinator).

1. Assessing Information Needs a. Continue asking key user groups what would be helpful information learned through

25 monitoring. (Coordinator and Grad Student) b. Continue tracking data use. Who is using what? (Coordinator and Grad Student)

2. Identified Gaps and Needs a. Coordinate the development of a methodology, including the process of identifying indicators or ‘eloquent species,’ for assessing key biological communities. Partners include at a minimum the Friday Harbor Labs, Kwiaht, the REEF program, SeaDoc Society, and WSU Beach Watchers. Modeled after the Indian Island Marine Health Observatory, or Waldron template, this would include surveys by volunteers, plankton and camera tows, and REEF surveys further offshore. An additional model is the Rapid Shoreline Assessment protocol conducted through People for Puget Sound several years ago. (Coordinator) b. Work with other regional MRCs to petition the NW Straits Commission and Puget Sound Partnership to provide support for a community monitoring QAQC process. (MRC and Coordinator) c. Continue to refine and prioritize data needs and gaps. (Group)

3. Prioritizing Monitoring Efforts a. Identify the specifics of monitoring that is required of SJC, who is doing what, overlaps, gaps, needs, partners, and funding potential. (Group with coordinator) b. Identify how monitoring needs called out in planning efforts interrelate, who is doing what, overlaps, gaps, needs, partners, funding potential. (Coordinator and Group) c. Identify who is best suited for specific monitoring priorities. (Group) d. Develop a local prioritization process that has buy-in from both monitoring groups and user groups. This may include a ranking matrix, a flow chart, a series of questions, or a combination. (Group) e. Add the Adaptive Management and Monitoring salmon recovery elements to this strategy as they become available. (Coordinator) f. Continue to incorporate terrestrial information into the MSA monitoring plan. (Coordinator and Grad Student)

4. Supporting Effective Existing Monitoring Efforts a. Work with community monitoring groups (e.g. Kwiaht, WSU Beach Watchers, SJC Land Bank, SJ Preservation Trust, SJ Nature Institute) to help integrate these efforts into the Prioritized Monitoring Strategy. (Coordinator and Grad Student) b. Identify how to “add value” to existing monitoring programs and incorporate these ideas into program implementation and funding applications. (Group) c. Coordinate with the federal and state agencies developing monitoring and assessment protocols to bring those tools to San Juan County. (Coordinator)

5. Establishing Monitoring Networks a. Enlist the support of existing and potential monitoring partners. (Coordinator and Group) b. Encourage academic institutions (U.W., Huxley College, Western, Skagit Valley College, WSU, and University of Victoria) to incorporate San Juan Islands’ monitoring needs into masters and PhD thesis programs. (Coordinator)

26 c. Facilitate useful partnerships, coordinate with all levels of monitoring groups, and work towards streamlining monitoring efforts. (Coordinator and Group) d. Coordinate this strategy with the implementation of local action agendas, management plans, and outreach/educational efforts. (Coordinator and Group)

6. Providing Access to Monitoring Information a. Summarize prioritized monitoring efforts and results for MRC’s website. Make sure that links are posted on key websites - SJC, Labs, local libraries, NGOs, state, feds. (Coordinator and Grad student) b. Publish monitoring results “fact sheets” in local newspapers, web news, key websites. (Coordinator) c. Give presentations of key monitoring information to decision makers and community groups. (Coordinator) d. Monitoring Workshop – partner with Islands Trust on a transboundary workshop, possibly in conjunction with the annual Marine Managers or Salmon Recovery workshops. (MRC and Coordinator) e. Include a “monitoring update” component in the local annual Stewardship Fair, County Fair, and other events. (Coordinator) f. Update the draft Marine Stewardship Area Monitoring Plan Excel table that to date includes primarily marine monitoring projects conducted in the San Juan Islands. (Coordinator and Grad Student) g. Partner with other MRC’s in the Puget Sound Region and work with the NW Straits Commission and Puget Sound Partnership to fund needed monitoring infrastructure. (MRC and Coordinator)

7. Finding Funding Support a. Develop a timeline for upcoming grant opportunities that include prioritized monitoring components. (Coordinator and Group) b. Communicate with potential funders, and assist partners in coordination of applications. (Coordinator) c. Find funding for the training and coordination of volunteers involved in local community monitoring efforts. (Coordinator and Group) d. Coordinate at all levels to identify common needs and partner in funding requests. (MRC and Coordinator)

27 Part II

Ecosystem Monitoring – a SUMMARY of local efforts in San Juan County

This document accompanies the San Juan County Marine Stewardship Area (MSA) Monitoring Plan. It is meant to be a guide to current locally based monitoring efforts, and incorporates projects related to marine, nearshore and freshwater habitats. A more comprehensive Excel document, MRC’s Monitoring Database, can be found in Appendix D and contains past and ongoing monitoring efforts conducted by local, regional, state, tribal, federal and transboundary agencies and organizations in the San Juan Islands. Most terrestrial components of both the Summary and the Plan are yet to be included.

There are four key components to the effective ‘adaptive management’ of ecosystems: Monitoring Outreach & Education Enforcement Restoration & Protection Monitoring provides essential data for all of the other components, as well as giving an indication of whether or not chosen actions are working. Our shared ecosystems are impacted by both legislation (county, state and federal) and by the choices each of us make about which products to use and what practices to follow for our boats, property and automobiles, and in our homes, gardens, barns, backyards, fields, forests, and businesses.

The following table shows locally based ecosystem monitoring (marine, nearshore, freshwater) or related efforts that 1. are currently active and fulfilling a goal/s of one or more of the following local planning processes, OR 2. have been identified as a need in San Juan County by one or more of the following local planning processes: Pilot Stormwater Monitoring Plan Marine Stewardship Area Management and Monitoring Plans San Juan Chapter (WRIA 2) of the Puget Sound Chinook Salmon Recovery Plan Shoreline Master Plan updates (San Juan County; Town of Friday Harbor) SJC Action Agenda (a chapter of the Puget Sound Action Plan) and local Implementation Committee efforts SJC Critical Areas Ordinance update Water Resources Management Plan for WRIA 2

The effectiveness of plan implementation is determined by monitoring! And accurate baselines are a must. Important as ecosystem monitoring is known to be, funding is often very difficult to secure. Note that funders can “add value” to local efforts by contributing to specific aspects of ongoing monitoring efforts, or by supporting currently unfunded efforts that have been identified through local planning processes as “needed.” In return, local programs cover parameters and/or locations not being monitored by wider efforts. Partnering at all levels increases outcomes and decreases redundancy.

Monitoring by nature requires a long term commitment of resources including time, people and money. Programs at all levels (local, regional, state, national and trans-boundary) often rely upon community volunteers. The synergy of involving community members not only increases the amount and type of data collected, it also geometrically increases outreach and education, while decreasing the need for enforcement actions.

All of the following efforts have been identified as “NEEDED,” therefore, if the monitoring effort has a current status of “Unfunded,” funding is needed to continue or to start up. If an effort has a status of “Ongoing,” additional funding may well be needed to continue or expand the effort to meet the goals of one or more of the above listed plans. TABLE 1. Local Ongoing Monitoring in the MSA

Adults accompany grade school students Acronyms on following page FH = Friday Harbor gs = graduate students PA = Preservation Area (voluntary) Volunteer Monitoring Effort Status Principle/s Needs Component 

Beach Watchers (BW) Continue basic operations, including training and coordination of Ongoing San Juan WSU Extension Adults projects throughout SJC volunteers Community Science Groups; Waldron; Kwiaht & BW for 3 Coordination; maintenance of existing sites; nets, equipment Ongoing All ages Marine Health Observatories MHOs & Lopez Salmon Team storage Project specific – training, coordination, supplies, equipment, Projects throughout SJC Ongoing Friends of the San Juans (FSJ) Adults analysis, synthesis 

 Marine Water Profiles Ongoing FH Labs; FSJ gs; FSJ  Sediments Ongoing Kwiaht BW, MHOs  Stormwater; parameters & sites SJC Stormwater Utility; Begin 2011 Adults limited due to funding Mike Kaill (Port FH aquarium)  Stream Health-longest fresh Unfunded FH Labs w/ Schools 4th grade, BW Reinitiate program; collection of flow data; synthesis water WQ data set in SJC 

Stream Typing Ongoing Kwiaht MHOs, BWs Long term monitoring Rocky Intertidal Ongoing FH Labs; FSJ; Kwiaht gs; FSJ; BW, MHOs Establish baselines; synthesis of data Rocky Sub-tidal Ongoing FH Labs; Kwiaht gs; BW, MHOs Establish baselines; synthesis of data 

FSJ; gs; Site specific monitoring; 5-10 year updates for countywide Eelgrass, Kelp, Seagrasses Ongoing FSJ; FH Labs; Kwiaht BW, MHOs assessments Invasive Clams Ongoing FH Elementary School 3rd grade Increased coverage Killer Whales- Southern Beam Reach; Center for Whale Ongoing gs; adults Program maintenance resident & transient Research; Orca Sound; TWM Forage Fish (Pacific Sandlance gs; FSJ; Further identification of spawning beaches; other life history Ongoing FH Labs; FSJ; Kwiaht & Surf Smelt) BW, MHOs stages; periodic updates of previous surveys Phytoplankton, Zooplankton Ongoing Beam Reach; FH Labs; Kwiaht gs; BW, MHOs Program maintenance, increased coverage MRC; FH Labs; Kwiaht w/ BW, MHOs; gs; Rockfish, Lingcod, Greenling Ongoing Increased coverage in & out of voluntary Preservation Areas schools 7th & 8th grade Establish baselines Seabirds Ongoing FH Labs; Kwiaht gs; BW, MHOs

Volunteer Needs Monitoring Effort Status Principle/s Component Current and Potential (?) Funding Avenues 

Shoreline Structures – shorelines around major islands Ongoing or Restoration Projects FSJ; Kwiaht FSJ; BW, MHOs Pre & post for specific projects; long term monitoring Unfunded Shoreline Modification Survey Unfunded Friends of the San Juans (FSJ) FSJ, BW Periodic updates (5-10 years) 

Project and Issue Specific Ongoing Stewardship Network BW, MHOs Continued coordination; outreach materials and workshops

30 Funders and/or Partners with their Acronyms Current Funders = $$ and are in bold; Potential Funders = ($$); Current Partners are in bold

Local Agencies, Districts and Advisory Committees State Agencies and Higher Education Open Space Advisory Team ($$) Department of Commerce = Lead Agency for EPA funding $$ Port of Friday Harbor ($$) Department of Health = Lead Agency for EPA funding School Districts – Lopez, Orcas, San Juan, Shaw $$ Department of Ecology (Ecology) = Lead Agency for EPA funding; $$ SJC Beach Watchers-WSU Extension (BW) Puget Sound Ambient Monitoring Program ($$) SJC Environmental Health Department ($$) Department of Fish and Wildlife = Lead Agency for EPA funding ($$) SJC Community Development & Planning Department $$ Department of Natural Resources (DNR) = Lead Agency, EPA funding ($$) SJC Land Bank $$ Recreation and Conservation Office (RCO); Salmon Recovery Funding Board ($$) SJC Lead Entity for Salmon Recovery WRIA2 (SRFBoard) $$ SJC Marine Resources Committee (MRC) $$ Sea Grant SJC Public Works Skagit Valley College $$ SJC Stormwater Advisory Committee $$ Washington State University (WSU) ($$) San Juan Islands Conservation District ($$) Western Washington University; Shannon Point Marine Lab $$ Stormwater Utility $$ University of Washington (UW) ($$) Town of Friday Harbor ($$) Water Resources Management Committee State NGOs $$ Wild Fish Conservancy Local Non-Governmental Organizations (NGOs) ($$) Washington Water Trust $$ Beam Reach Chambers – San Juan, Orcas, Lopez Tribal $$ Center for Whale Research ($$) Lummi Nation, Samish Nation, Swinomish Indian Tribal Community, Tulalip Tribes $$ Friends of the San Juans (FSJ) $$ Orcas Island Community Foundation Federal Agencies Private local schools ($$) Army Corps of Engineers (Corps) $$ Kwiaht ($$) Bureau of Land Management (BLM) ($$) San Juan Community Foundation $$ Environmental Protection Agency (EPA) San Juan Nature Institute ($$) National Marine Fisheries Service (NMFS) San Juan Preservation Trust $$ National Oceanic and Atmospheric Administration (NOAA) San Juan Visitors Bureau ($$) National Park Service (NPS) $$ The Whale Museum/Soundwatch Program (TWM) $$ National Science Foundation (NSF) ($$) US Fish & Wildlife Service Regional Agencies and Programs ($$) US Forest Service ($$) Estuary and Salmon Restoration Program (ESRP) ($$) US Geological Survey (USGS) $$ Northwest Straits Commission ($$) Puget Sound Nearshore Ecosystem Restoration Project (PSNERP) National NGOs $$ Puget Sound Partnership ($$) Audubon Skagit Fisheries Enhancement Group $$ National Fish & Wildlife Foundation (NFWF) Regional NGOs $$ The Nature Conservancy (TNC) $$ People for Puget Sound Reef Environmental Education Foundation (REEF) ($$) Puget Sound Restoration Fund ($$) SeaDoc Society $$ The Russell Family Foundation

Part III Monitoring Plan for the Marine Stewardship Area: Status, Research and History

1. Introduction

1.1 What is the Marine Stewardship Area, and Where is it Located?

The Marine Resources Committee (MRC) is a citizen advisory committee appointed by the San Juan County Council. The MRC receives Federal Coastal Zone Management funding administered by the Washington Department of Ecology and by the Northwest Straits Commission. The MRC developed and implemented the Marine Stewardship Area Plan (MSA Plan), approved by the County Council in 2007. They also fund research for the MSA, and provide public education and outreach. During 2004-2006, the MRC developed a plan for the Marine Stewardship Area, following the 5-S planning process developed by The Nature Conservancy (Poiani et al. 1998, 2000, Parrish et al. 2003).

The San Juan Board of County Commissioners (now County Council) designated the waters of the entire County a Marine Stewardship Area (MSA) with the stated objective: “to facilitate the protection and preservation of our natural marine environment for the tribes and other historic users, current and future residents, and visitors” (MSA Plan, 2007). With this resolution, the Marine Resources Committee (MRC) was charged with providing a formal study with detailed recommendations for achieving this goal. The MRC thus began collecting and mapping available marine resources data to get a better picture of San Juan County’s marine life, and habitats, as well as potential measures that would help protect them (Klinger 2001ab, 2006).

During the year following the designation of the MSA, the MRC developed the concept for a county-wide zone scheme (Slocomb 2004). The MSA plan proposed special use areas along county shorelines where particular resources were found to be abundant. The proposal included multiple use and restricted use areas, and set out voluntary protection measures such as not anchoring in eelgrass beds and not fishing in Bottomfish Recovery Areas. MRC funding has been used to assess the effectiveness of these recovery areas through 2006.

It is important to recognize that the San Juan County MSA exists within the broader Puget Sound Region (PSR) (sometimes referred to, incorrectly, as Puget Sound), defined here as the marine waters of Washington State east of the mouth of the Strait of Juan de Fuca. Within this region, there are five recognized PSAMP basins (PSAT 2007, PSS 2011, Fig. 1-1), including the “San Juan Archipelago” basin, which is approximately equivalent to the MSA. The Puget Sound Region, along with the Strait of Georgia to the north, is sometimes referred to as the “Salish Sea” (i.e. all waters enclosed by Vancouver Island and the Olympic Peninsula, from Tumwater WA to Johnstone Strait British Columbia).

Alternatively, the DNR submerged vegetation monitoring program (SVMP) refers to this area as the “San Juan Straits Region” (including the Strait of Juan de Fuca and the MSA), bordered by the North Puget Sound Region to the north and east, the Saratoga-Whidbey Region east of Whidbey Island, the Hood Canal Region and the Central Puget Sound Region to the south of the San Juan Straits Region (PSAT 2007, PSS 2011, Figs. 2-4, 2-7.). Clearly the nomenclature of the region is ambiguous. That said, the San Juan Archipelago, and the Gulf Islands to the north, have ancient significance, as discrete regions, to the Coastal Salish native peoples (Suttles 1951). The Puget Sound Partnership has also established a list of seven Action Areas that correspond to some of the regions defined above (http://www.psp.wa.gov/aa_action_areas.php). They are: Hood Canal, North Central Puget Sound, San Juan/Whatcom, South Central Puget Sound, South Puget Sound, Strait of Juan de Fuca, and Whidbey.

Marine Protected Areas in the MSA. It should be noted that the waters of San Juan County and Cypress Island were previously designated a Marine Biological Preserve in 1923 (Chap. 74, House Bill 68, R.C.W.28.77.230, 1969 Revision R.C.W.28B.20.320), specifically for “marine biological materials useful for scientific purposes, except when gathered for human food, and except, also, the plant Nereocystis….” , with permission for collecting to be “… first granted by the director of the Friday harbor Laboratories of the University of Washington.” This Marine Biological Preserve designation is still in effect and scientific collecting of non-food species has been approved annually by the director of FHL since 1923.

Within the MSA, there are also designated Marine Preserves managed jointly by WDFW and the University of Washington, in which bottom fishing and harvesting of benthos is not allowed (Pt. Caution, SJI, Pt. George, Shaw Is., False Bay, Argyle Lagoon; only trolling for salmon is allowed) or where no fishing is allowed (Yellow and Low Islands). For MPA designations in general see Kelleher et al. (1995) and Klinger (2004), and for those in Washington State, see Didier (1998) and Klinger (2007). Other protected areas include the Federal Wildlife Areas (for birds, marine mammals), which are mostly rocky islets with a 200m no-go zone around them, providing de facto protection for the shallow marine zone.

1.2 Need for A Monitoring Plan

Despite the best efforts of the MRC to document the county’s marine resources, data do not exist to accurately assess the status or trends of all marine resources within the MSA. A particular shortcoming is that, frequently, data are only sufficient to describe the status of a particular species at one point in time and/or at one or very few sites. This attribute of existing data handicaps efforts to determine the current status of knowledge regarding species, habitats and communities and prevents an analysis of trends related to the threats from human activity and development. Moreover, the influence of environmental change resulting from the predicted shift in hemispheric and regional climate (e.g. warmer temperatures, wetter winters) on the range and distribution of native species, the spread of invasive species and of diseases may not be detected. This MSA Monitoring Plan outlines the need for additional descriptive information for marine species and the habitats in which they thrive, and advocate systematic monitoring of selected parameters designed to yield status and trends information for benthic and pelagic habitats.

Without a good monitoring program, valuable ecosystem services may not be protected, thereby jeopardizing the sustainability of the MSA. We understand funding is limited and that a systematic and sustained monitoring program cannot rest solely on the volunteer labor or over- committed county staff. Fortunately, a number of monitoring programs already exist throughout the Puget Sound Region, detailed in the Puget Sound Ambient Monitoring Program and other recent compilations. In some cases, these programs are adequate to evaluate impact to the MSA (e.g. spawning biomass of Pacific herring, adult salmon populations, pinto abalone abundance, and resident orca populations), and in other cases, while there is a reasonably adequate regional

33 monitoring program, data collection within San Juan County is not sufficient to evaluate impact within the county. In the latter case, it may not be sufficient to rely on federal or state programs to adequately monitor benthic and pelagic systems within the MSA. Rather, federal and state monitoring programs, augmented by a county sponsored program, will be needed. There are also situations where a resource is monitored within the MSA, but at only one or a few sites; locally funded programs can enhance ongoing population monitoring. Finally, there will be many cases where species or groups of species, found to be locally important fall outside existing monitoring programs, and our task will require designing a program to adequately protect ecosystem health and biodiversity within the MSA.

1.3 Monitoring Versus Assessment

Inventories or baseline studies attempt to establish the composition of populations, biotic communities, or habitat types so that their status may be compared at a future, sometimes undetermined, time. It is often understood that regular, sustained monitoring may not be possible. Such inventories have multiple goals, such as mapping populations by species or habitats, determining population densities, assessing age distributions ), ,assessing habitat requirements of a species, and assessing existing or potential threats to a population or community (Elzinga et al. 2001). This activity is distinguished from natural history studies or hypothesis-driven ecological research that investigates population viability, mortality, predator- prey interactions, life history variability, behavior, trophic transfers, or other specific questions.

Monitoring, which occurs over more than one time period, may also be variable in its intent and purpose. Implementation monitoring examines whether a particular activity affects some subset of the biota, which could be for a single population (e.g. whale watching on orca whale behavior) or an entire community or habitat type (e. g. compliance with Washington State Hydraulic Project Approval when shoreline construction is proposed). Such monitoring might be carried out until funding is completed, regulatory conditions are met, or a particular question is answered to the satisfaction of the researcher or the funding agency. Such studies are often termed impact studies, when designed to measure the impact of a stressor or perturbation. A variety of impact study designs are discussed by Murray et al. (2006); one common example is the BACI design simply described as the collection of data from control and impact sites, before and after the impact occurs (Green 1979, Hurlbert 1984, Underwood 1994, Osenberg and Schmitt 1996, Osenberg et al. 1996).

Monitoring programs often begin with a single survey or inventory. This activity may also include the acquisition of historical data within the study area, which results in a patchy data series before the initiation of a full monitoring program. There is always a question of what “baseline” to use for comparison, since we know that biotic communities change composition over time. Furthermore, even if we wanted to establish a baseline of 300 years ago, we know there are essentially no data to provide one. The concept of “shifting baselines” describes how each human generation adapts to current conditions, whereas there may have been ecological changes that have not been recorded or documented (Jackson et al. 2001, http://www.shiftingbaselines.org/slideshow/index.html). For the Puget Sound Region, shifting baselines have been illustrated in a 2008 video presentation (Olson 2008, PSP website: http://www.psp.wa.gov/shiftingbaselines.php).

34 Once a monitoring program is initiated, the goal is to maintain the same spatial and temporal sampling pattern, and it may also be important to set temporal endpoints that are ecologically meaningful (Karr and Chu 1997). Several authors note the importance of designing a monitoring program capable of detecting change over pre-defined short to long temporal scales, with adequate spatial replication to evaluate resource conditions within the region of interest (Kingsford 1998, Kingsford and Battershill 1998, Kingsford et al. 1998). In this case the objective is to consider the entire MSA as the region of interest and design monitoring programs capable of detecting change within this area, and determining whether that change is significant.

Database of Monitoring Efforts in the MSA. An important part of developing a monitoring plan was the identification and listing of all monitoring programs, regardless of status, that have occurred or are occurring in San Juan County. In Appendix D, we list, in a database format, all existing programs being conducted by federal, tribal, state and county governments and NGOs such as Friends of the San Juans and The Nature Conservancy. In the excel database, programs that have been terminated are listed. We strongly suggest that the future monitoring of the MSA targets must include the continuation of ongoing programs as well as the selective resumption of programs that have been terminated. Locations of monitoring efforts, based on this database, are given in Figures 5-8.

Existing monitoring programs and surveys within the PSR are well described in the PSAMP Update (2007); see also Truscott (2004) and Mumford et al. (2004), Mitchell and Ford (2004).

1.4 Targets, Communities, and Biodiversity

Targets of the MSA Plan are defined as those groups of species and communities that are critical to conserve and protect ecosystem services and biodiversity within the MSA, and which must be monitored to determine their current status and direction of change. Some targets are chosen because the distribution and density of these species or communities are poorly known but population stability is threatened by activities that are increasing (e.g. bycatch associated with fish harvest, stormwater discharge over intertidal communities). Others are targets because the link between human activity and species decline has been established (e.g., recreational harvest of groundfish, impact of overwater structures on nearshore benthic plant survival and juvenile fish migration). The MSA Plan identifies the following targets:

- Rocky intertidal communities - Rocky subtidal communities - Nearshore sand, mud and gravel communities - Rockfish, lingcod and greenling - Seabirds - Marine mammals - Pacific Salmon, forage fish

For each of these targets, the MSA Plan also identifies key ecological attributes (KEAs), or indicators, which are either species, groups of organisms, or chemical/physical processes which allow an assessment of ecosystem stability and biodiversity. The MSA Plan also sets out three socio-cultural targets involving human use of the marine environment and various species. They are:

35 - Enjoyment of the marine environment - Support for marine-based livelihoods - Maintenance of Cultural traditions including ceremonial, subsistence, and spiritual uses and aspects

In addition to targets noted above, the MSA plan also identified and defined sixteen threats affecting marine biodiversity targets within the MSA (Table 2, MSA 2007). These threats must also be monitored to determine their persistence and importance, to document the trajectory of influence and evaluate the effectiveness of regulations designed to protect ecosystem services and biodiversity.

In general, monitoring programs target individual species, sometimes termed indicator species. Such species can be chosen because they are (1) abundant and characterize the habitat or community, (2) charismatic, (3) rare and at risk of local extirpation or extinction, (4) respond negatively to environmental stress or perturbation, or (5) commercially important. Expanding a monitoring program to include other species may be appropriate because results of ongoing research identify these species as important indicators of ecosystem change (e.g. use of lichen communities to monitor air quality).

Managers and researchers are challenged in that a community contains hundreds to thousands of species, and it is not possible or desirable to monitor all species present. Consequently, well defined criteria must be established to direct sampling from which spatial and temporal generalizations can be made. Management of marine resources is increasingly viewed from an ecosystem perspective (ecosystem-based management), recognizing that single species management is not sufficient to detect ecosystem changes or to identify potential impacts of human activity. Interactions among predators and prey, switching to alternate prey, and responses to changes in the chemical and/or physical environment, all affect community composition and ecosystem function. So, even if target or indicator species are identified, change or lack of change in those species is not sufficient to understand change (or loss of function) at the level of the community or ecosystem.

The objective of biodiversity monitoring is to determine species composition and relative abundance within a specified area, community, or habitat. Ideally, we would like to have data for all species present, but that is rarely possible. Effective monitoring determines which species indicate population stability and biodiversity, are easy to identify, and are representative of larger groups. Some monitoring protocols combine rapid field assessment and substantial taxonomic lumping, with extensive collections that can provide accurate species identification at a later date (e.g. NAGISA, http://www.coml.org/descrip/nagisa.htm) if needed. One problem with focusing on target or indicator species is the potential to miss changes, such as range extension or restriction, associated with climate change among non-target organisms.

Monitoring may not be sufficient to describe proximate controls on community structure. For several decades ecologists have recognized that field experiments may be necessary to quantify processes that determine community stability and resilience (Paine 1974). Strong biotic interactions such as competition and predation are constant in space-limited communities such as in rocky intertidal and subtidal habitats (Sebens 1986, 1990), and soft sediments (Reise 1985, Volkenborn and Reise 2006). Although community structure may seem stable, this condition may be a balance between predation by competitively dominant species and the constant influx of less dominant species. The experimental clearing of space, such as the removal or addition of

36 predators and competitors, and the manipulation of environmental conditions are often necessary to understand community interaction and the resulting structure. While not part of a monitoring program, such research is key to an understanding of population stability and biodiversity. To enhance the understanding of ecosystem function, this type of investigation should be encouraged, and carried out by researchers in parallel with monitoring programs.

Monitoring socio-cultural targets presents additional challenges as the primary data are population abundance estimates, collected by natural resource agencies, and harvesting and gathering records, required by resource agencies, but submitted by those who fish and collect the resource in question. While in some cases there is a direct link between harvesting practices or frequency (e.g. the impact to groundfish stocks) this is not always the case. For example, reduction of forage (this term has been defined above) fish such as Pacific herring, sandlance, and surf smelt, may be more a function of altered habitat than of fishing pressure. Because fishing pressure may also reduce Pacific salmon population abundance, the task of assigning proximate cause, and resultant regulatory action, becomes difficult. To offset this difficulty multiple monitoring programs may be necessary. Data from marketing-based surveys and local income assessment from marine-based livelihoods should be considered in assessing impacts and determining sustainability. In the Puget Sound region, there has been a shift in marine-based livelihoods from resource extraction to ecotourism activities such as whale watching, sea kayaking, and tide pool viewing.

Monitoring known threats to the MSA represents an additional layer of complexity. The MSA Plan identifies 16 threats (Table 1). Ongoing federal and state programs (PSAT 2007, PSS 2011) track the relationship between stressors, such as chemical contamination and overfishing (Table 1), and the abundance and distribution of particular species, and monitor the condition of pelagic and benthic habitat (e.g. WDNR’s Submerged Vegetation Monitoring Project). The impact of other activities, identified as threats (e.g., stormwater runoff and shoreline armoring; Table 1), however, may not be adequately evaluated in some areas at present. Consequently, local efforts are needed to fill important gaps and insure population stability and biodiversity is maintained within the MSA.

1.5 Parameters to measure – abundance, life history, harvest etc.

For any species, numbers of individuals or biomass are common measures of abundance, but these metrics may only provide partial information on the vitality of the population. If we want to know if a population is increasing, decreasing, or stable other metrics may be necessary to track ecosystem condition. For example demographic indices such as life tables, reproductive rates, growth and size structure, are additional measures that index biological responses to environmental conditions and changes in conditions. For some species, such as clonal plants and colonial animals, the differentiation of individual units is difficult to determine; thus measurements such as percent area covered (percent cover) are commonly used as indices.

Table 1. Top threats affecting all marine biodiversity targets in the San Juan County Marine Stewardship Area (as of 8/31/06) *designates tied ranking. (see Table 2, MSA Plan 2007)

Rank Threat Overall

37 Rank 1 Large oil spills High 2 Climate change High 3 Shoreline modification, e.g. docks, shoreline armoring, High boat ramps, jetties, etc. 4 Non-local sources of salmon decline High 5 Invasive species Medium 6 Persistent organic pollutants from current and historical Medium sources 7 Polluted stormwater runoff Medium 8 Septic systems and wastewater discharge Medium 9 Predation by marine mammals Medium 10 Historical fish harvest (e.g. rockfish, lingcod & Medium greenling until 1999) 11 * Disturbance by other wildlife Medium 12 * Fishing/harvesting activities Medium 13 Derelict fishing gear Medium 14 Small chronic fuel and oil spills Medium 15 Human disturbance on shore Low 16 Sediment loading from upland construction activities, Low logging, clearing and livestock

Overall Threat Status for MSA - High

It is a continuing challenge to obtain an accurate estimate of population abundance of commercially harvested resources. One source of data on the status of population abundance is harvest data, a practice that assumes the original population abundance (pre-harvest) is a baseline and decreasing harvest (catch per unit effort) indicates a declining population. Increasing harvest effort is a common feature when and if the marketplace can support the distribution of more product, in this case, marine fishes such as rockfishes (Sebastes spp.). However increased yield could also be related to stock recovery, and thus an increase in population size might be taking place (e.g. lingcod, Ophiodon elongatus). Theoretically, those who commercially fish could determine the optimal population density that provides the greatest yield, by trial and error - sometimes overshooting the optimum and catching less, and sometimes undershooting it and also catching less, and sometimes undershooting it and also catching less.

1.9 Information Management Strategy

Conservation priorities determined by the SJC MSA Plan followed a consensus building approach based on The Nature Conservancy’s “Five-S Framework for Site Conservation” (Anonymous, 2000). The fifth and last step in this methodology is designed to measure the success of their implementation over the following decade(s) through a series of monitoring objectives – this necessitates an information management strategy for the SJC MSA Monitoring Plan.

38 A data standard is offered with the Five-S Framework for assessing the viability of species and ecological communities (Howie, et al., 1999) that is based on the Element Occurrence (EO) Data Standard (Anonymous 2002). An EO is a geographic region within which a species or natural community exists. Correspondingly, an EO record is a data management tool that has both spatial and tabular attributes and is the basis for the standard. The EO Data Standard has recently been amplified and extended to include individual observations, for example, those provided by citizen science efforts like the Audubon Christmas Bird Count (John Gamon, personal communication).

Since 2001, the non-profit conservation organization NatureServe, together with its network of natural heritage programs and data centers from all 50 U.S. states, Canada, Latin America and the Caribbean, has moved forward the data management and analysis initiatives developed by The Nature Conservancy – a cornerstone of this network is the EO Data Standard. One relevant example of the EO reduced to practice is the NOAA Coastal and Marine Ecological Classification Standard implemented in partnership with NatureServe (Anonymous, 2010).

Because the SJC MSA Plan is based on the Five-S Framework and the EO Data Standard has been widely adopted for conservation priority assignment and management, the NatureServe implementation provides a reference point for discussion of the SJC MSA Monitoring Plan’s information management requirements and strategy.

The SJC MSA Monitoring Plan is not, however, obligated to use the EO Data Standard. Indeed, this standard was developed for terrestrial-based environmental systems for determining and assigning conservation priorities, and may not be suitable in some cases for related purposes or for marine-based environmental systems.

A formal requirements analysis is recommended at this stage in the overall process to determine our scope and needs.

Challenges and Opportunities. The central challenge we face when creating an information management strategy is cost as a barrier to entry. The expense of capitalizing an information system together with the personnel required to curate and administrate it over time far exceeds the currently available budget.

Additionally, the requirements of the information system, as initially provided by the conservation and socio-cultural targets determined by the Five-S Framework process and described in detail starting on page XXX, are broad in scope. The challenge here is to generalize and integrate data across scientific disciplines from studies on marine mammals to phytoplankton, from finfish to seabirds, from shoreline community ecology to land-based stormwater runoff, and bioaccumulation of toxins in the marine environment and its’ resident organisms. Data contributed to this information system are acquired by federal, state, local, university and citizen science –based efforts.

A further challenge is legacy data. A rich and important source of information, these data exist in a variety of formats, across a range of goodness and standardization. These data may come from UW-FHL investigator initiated scientific studies or from a wide variety of other sources. See Appendix D for a partial catalog of current and legacy monitoring efforts within the SJC MSA region.

Considering these challenges, an opportunity may exist because of scale, which may in turn provide a possibility to partner with and leverage other information management initiatives. For example, the requirements of this SJC MSA Monitoring Plan are likely to overlap with those faced by other MRC’s,

39 and together as a group we may be able to leverage the resources of initiatives like NatureServe or the Northwest Association of Networked Ocean Observing Systems (NANOOS). A leveraged approach at a larger scale may not only help to overcome cost as a barrier to entry, but also provide greater utility to a broader user community.

Requirements Analysis. A requirements analysis represents the ‘users’ perspective on the scope and needs of an information management system (Berenbach, et al., 2009). It is used to manage the transition to a ‘developers’ perspective.

A formal requirements analysis is recommended here that is based on the outcome of the Five-S Framework effort and the established conservation and socio-economic targets and benchmarks. In addition to consideration of relevant data, importantly, this analysis would also determine the requirements of the user community. It would also provide an outline for scope of the systems’ curation and administration.

Performing a formal requirements analysis itself does not need to represent a barrier to entry. An agile approach can be used to reduce unnecessary complication (Larman, 2004). The scope of the analysis can be readily tailored meet the needs of this SJC MSA Monitoring Plan and/or be expanded to include other MRC’s.

Monitoring. At the present time there is an immediate need to provide a data standard for active monitoring programs. This data standard is designed to support the maintenance of the Catalog of Monitoring Efforts Within the SJC MSA Region that is included in Appendix D. See Appendix B for a revised version of the supporting SJC MRC Monitoring Plan GIS Data Standard from 2009.

A current methodology for using the NatureServe EO Data Standard is available together with an accompanying Excel® -based workbook (Faber-Langendoen, et al., 2009). This provides additional detail for evaluating the EO Data Standard and its’ suitability for use as part of this SJC MRC Monitoring Plan.

If the SJC MSA Monitoring Plan does not adopt a data standard it will be necessary to implement one.

Key Considerations. Watersheds – Of the nine (9) conservation and socio-economic targets determined by the SJC MSA Five-S Framework process, six (6) include a benchmark that is based on stormwater runoff and watersheds. Additionally, upland water quality and stormwater management are identified as a top-tier initiative by public review of SJC MSA Plan and there is overlap with the SJC Stormwater Utility.

Historically, SJC Department of Health and Human Services has based water quality studies on a nine (9) watershed scheme (Tompkins et al., 2000; Weisman, et al., 2000). Presently, the SJC Public Works GIS unit has an updated working watershed scheme based on a digital elevation model created from 2009 LIDAR dataset. This working watershed scheme can be viewed on the SJC Stormwater GIS Pilot project website (XXX). Here we recommend that a final watershed scheme be published for SJC.

Shoreline Segment Identification - Of the nine (9) conservation and socio-economic targets determined by the SJC MSA Five-S Framework process, three (3) include a benchmark that is based on the impact of armored shoreline segments which extends to anthropogenically degraded shoreline segments. There is an overlap here with the pending SJC Shoreline Master Program and SJC Critical Areas Ordinance updates.

40 To support the identification of shoreline segments landscape scale data are required and are available from a variety of sources. Examples include, but are not limited to, the WA Department of Natural Resources (WDNR) Shorezone which is based on shoreline geomorphology (Berry 2002), the WA Department of Ecology (DOE) Marine Geographic Response plans for oil spill response website (refXXX), and the DOE Shorephotos that are available on a website (refXXX) that provides complete shoreline coverage using high resolution, geo-referenced oblique aerial photos. Here we recommend that a final shoreline segment identification scheme be determined and published for SJC.

. Preliminary Strategy. Steps that lead to determination of an information management strategy are listed here.

Under the direction of the Science Subcommittee:

1. Adopt an interim data standard for SJC MSA Monitoring project data.

2. Perform a formal requirements analysis, using agile methods, based on the SJC MSA Plan, where the outcome is a requirements specification document. This should include a list of relevant existing and planned datasets and GIS data layers with metadata where available, include a description of user requirements, and provide an outline for scope of system curation and administration. This document should be prepared with consideration for scale-up to include other MRC’s in a follow-on effort.

3. Perform a review of existing information management initiatives and projects that have a fit with marine-based environmental systems and conservation priorities. Determine possible interest in collaboration or subscription.

41 Preliminary list of information management system initiatives and projects of interest.

Name Type Description

NatureServe Initiative Supersedes TNC as the controlling organization for the network of natural heritage programs and clearing house for the EO Data Standard. Developers of the NatureServe Vista and Biotics software technologies. http://natureserve.org/

NANOOS Initiative Regional implementation of the federal U.S. Integrated Ocean Observing System (IOOS) http://ioos.gov. On-line data products and visualization tools. MOA emphasizes collaboration with a variety of organization types which would include MRC. http://nanoos.org.

Data Basin Initiative On-line community of shared conservation projects. http://databasin.org.

The Conservation Registry Initiative On-line community of shared conservation projects. http://conservationregistry.org

SQL Share Project On-line academic approach to solving the problem of dealing with disparate data and an undefined schema. No spatial features. http://escience.washington.edu/what-we- do/introducing-sqlshare

Sound IQ Project On-line example (CityIQ) for Bellingham, WA showing GIS implementation. http://www.cob.org/services/maps/online- mapping/index.aspx

SJC Stormwater GIS Pilot Project On-line rapid-development pilot project showing watersheds and relevant stormwater data layers. http://sjcgis.org/stormwater/default.aspx

4. Prepare a short-list of options for review and discussion by SJC MRC.

5. Determine the future direction of the information management strategy and prepare a plan for a Final Strategy.

Section 2. Ecosystems and Biological Resources

As part of this treatment we sought input from members of the Marine Resources Committee Science Subcommittee. Each member was tasked with compiling a list of elements they deemed integral to a monitoring program in their area of expertise. To augment and enrich this effort, we also interviewed a select group of regional scientists and resource managers using a structured interview format (Strauss and Corbin 1990; XXXother refs). This section synthesizes our results.

2.1 Overview Many of the species, habitats and ecosystem components discussed in this document have also been detailed in the San Juan County MSA Plan (2007) and the San Juan County Best Available Science for Critical Areas document (2007). For the broader Puget Sound Region, the 2007 Puget Sound Update (PSAT 2007, PSS 2011) is extremely informative. These three documents contain excellent maps of biological resources, habitats, protected areas and other data relevant to this monitoring program. This document will not undertake to duplicate all the information provided in the BAS document, but will be limited to discussion of existing monitoring programs, and recommendations for future monitoring. Background information, existing status, and information from other regions will be brought in as needed, but is not meant to be comprehensive.

2.2 Species and Groups of Concern The MSA includes species considered endangered or threatened, as well as species whose populations have declined significantly over the past century or over recent decades. While we are concerned with the biodiversity of the MSA overall, we will also pay particular attention to species whose populations are in danger within the MSA or within the broader region. Examples would be orcas, abalone, native oysters, eelgrass, rockfish, and Chinook salmon. Species and groups of concern are also set out as targets in Table 1 of the MSA Plan (2007). For the larger region, PSAMP (2007, Table 2-1) lists 63 “species of concern” in Puget Sound (Gaydos 2004), defining them as those species that “require special initiatives to ensure protection and survival of their populations”. Of these, three were invertebrates, 27 were fishes, 23 were birds, nine were mammals and one was a reptile. Fourteen of these species are defined as threatened or endangered by the federal government or by the state. Most, if not all, of these are species of concern for the SJC MSA as well.

2.3 Plankton (relevant MSA Target: Seabirds, Pacific Salmon) Plankton are single or multi-celled swimming or drifting organisms that form the foundation of marine food webs (Emmett et al. 2000) by serving as prey for a vast array of other species ranging from crustaceans, to fish, birds and whales. Plankton are a diverse group, grouped based upon their inability to swim against fluid motions and on their morphology, instead of genetic

43 lineage or taxonomy. In the MSA Plan, zooplankton (e.g. euphausids, crab larvae, amphipods) are identified as relevant to the Seabird target. Phytoplankton are photosynthetic marine algae that fix carbon, providing primary production for the pelagic food web. Abundance of phytoplankton fluctuate annually as a function of temperature, light, and nutrients, which can result in dramatic blooms that persist for days to weeks (usually during March to September, PSAT 2007, PSS 2011, Figure 2-1). In the San Juan archipelago and in the Puget Sound region, phytoplankton are predominately composed of diatoms in the fall and winter. Dinoflagellates dominate in spring and summer. Certain species of phytoplankton pose human health risks (e.g. red tide) and can be damaging to mollusks such as aquacultured oysters and fish. For studies of phytoplankton within the MSA see: Bernhard et al. (1997), Yin and Harrison (2000), Rines et al. (2002), Newton (2003), Broitman and Kinlan (2006). Zooplankton are animals that drift or swim and are divided into micro- or macrozooplankton based upon size. Microzooplankton comprise mostly copepods and crustacean larvae. Macrozooplankton include jellyfish, salps, ctenophores, and other groups. Larvae of benthic invertebrates are termed meroplankton, and fish larvae are ichthyoplankton. Those zooplankton that spend their entire life cycle in the plankton are termed holoplankton. Zooplankton make up the diet of some commercially important fish species and their prey. Forage fish (sand lance, herring, smelt) and juvenile salmon all consume zooplankton. Zooplankton studies from within and near the MSA include Simenstad et al. (1980), Buck and Newton (1995), Dagg et al. (1998), and (Mills 1993, 1995, 2001) for gelatinous zooplankton. Bacterioplankton include marine bacteria and those from freshwater runoff. Particular species are investigated as part of water quality monitoring for aquaculture and swimming beaches (e.g. Escherichia coli bacteria). Viruses in seawater comprise the viroplankton. Existing Monitoring. PSAMP regularly monitors the water column at seven locations within and around SJC. Dr. Jan Newton (UW) leads a fall Research Apprenticeship at UW FHL that conducts similar sampling during October to December of each year in the San Juan Channel and south of Cattle Point, and JEMS cruises sample at 5 sites across the Strait of Juan de Fuca. Friends of the San Juans carry out regular sampling at five points around San Juan Island, and at Fisherman Bay on Lopez Island. These sampling efforts quantify physical characteristics of the water column as well as the chlorophyll content (related to phytoplankton abundance), the types of phytoplankton present, and the abundance of zooplankton. Elsewhere in the Puget Sound Region, the Pacific Shellfish Growers Association monitors potentially harmful phytoplankton in embayments that are important to aquaculture (http://www.pcsga.org/pub/science/water_quality.shtm).

The National Oceanic and Atmospheric Administration (NOAA) has a major research investment in the state focused on understanding causes of harmful algal blooms (HABs) and using the information to help state agencies develop effective methods of monitoring and prediction (Cox et al. 2004). There is a short-term goal to minimize impacts of HABs and a long- term goal to understand causes of blooms that will improve forecasting capabilities and indicate prevention strategies. This research is conducted through three major National Center for Coastal Ocean Sciences (NCCOS) programs: the multi-agency Ecology and Oceanography of Harmful Algal Blooms Program (ECOHAB) focuses on causes of HABs; the Monitoring and Event

44 Response to Harmful Algal Blooms Program (MERHAB) focuses on protecting human health and minimizing impacts on coastal economies; and the Coastal Hypoxia Research Program (CHRP) focuses on developing modeling tools to assess hypoxia management strategies. NCCOS responds to HABs and conducts biotoxins research to complement extra-mural research programs ( http://www.cop.noaa.gov/stressors/extremeevents/hab).

JEMS cruises occur monthly from just south of Cattle Pt., San Juan Island, to north of Port Townsend on the Olympic Peninsula (using the UW FHL Vessel, Centennial). JEMS was important to MEHP because it provided data for Marine Protected Area (MPA) delineation and evaluation and was the only long-term time-series monitoring data from this key ecosystem. Monitoring of plankton was added to JEMS during its second phase, filling an unmet finding of the 1995 PSAMP review (Shen, 1995). The Strait acts as a conduit for dispersion and transport of plankton, including components such as larvae, invasive species, and harmful algal bloom species.

The transported volume of HAB algae species that produce domoic acid, from the Washington coast to Puget Sound is an on-going question (Homer et al. 1996, Wekell et al. 2000). Regionally, little is known about how variability in plankton species relates to the health of fish and higher organisms that feed on these algae For some local stocks of planktivorous fish such as juvenile salmon and herring, little research has investigated the effect of variation in plankton assemblages on fish diet and net energetic gain. Not only are plankton species assessments essential for food-web analysis, but exotic species are appearing in this area, with potentially profound ecosystem-level effects.

A citizen-led monitoring effort on Waldron Island quantifies zooplankton abundance and composition twice monthly in an effort to understand prey availability for juvenile salmon (from June 2007 – present) (Julia Lloyd, pers. comm.). Zooplankton and phytoplankton communities have been studied intensively for short periods in East Sound, Orcas Island (Refs.) to develop an understanding of plankton community diversity and processes that regulate abundance.

Proposed Monitoring. Monitoring of plankton within the MSA is seasonally discontinuous and does not cover more than a few sites within the region. One recommendation would be to continue the Pelagic Ecosystems (Research Apprenticeship, UW FHL, October-December only) monitoring throughout the year and to expand the number of sites visited from 2-3 to 5-10. This expansion would be the equivalent of repeating the monthly JEMS effort, and would include sites at the northern end of San Juan Channel, the central area of San Juan Channel, the northern end of the MSA and within some of the major embayments (e.g. Eastsound, West Sound, others). This effort, like most of what follows, needs more than just monitoring. There is a clear need for analysis and synthesis of this information, placing it in context of the food web.

45 2.4 Aquatic Vegetation Aquatic vegetation provides structure, habitat, and food for a wide variety of marine life. Aquatic vegetation is not evenly distributed across the San Juan Archipelago, often occurring in patches, and the growth of vegetation can quickly fluctuate as a function of nutrients, water clarity, and disturbance. Due to their rapid and easily visible response to stress, kelp and eelgrass are frequently identified as strong indicators of environmental health. a. Kelp and Other Marine Algae (MSA Targets: Rocky Intertidal Communities, Rocky Subtidal Communities) Kelp are marine algae in the order Laminariales, of which 23 species are found in Washington State (Gabrielson et al. 2006). They are among the largest and most productive marine macroalgae and frequently form beds and zones visible from shore or from the air. Kelp beds provide habitat for a variety of fish and invertebrates (Ghelardi 1971, Carr 1983, Murphy et al. 2000), and may be especially important as habitat for juvenile rockfish in the San Juan Archipelago (Hayden-Spear 2006). Moreover, in nearshore marine habitats kelp is a critical source of particulate organic material that is an important food source for many filter feeding invertebrates (Dunton and Schell 1987, Duggins et al. 1989). Kelp beds vary from site to site and from year to year in their extent, and are controlled by a suite of physical and biological factors (Carney et al. 2005, Duggins 1980, Dayton and Tegner 1984, Grove et al. 2002, Maxell and Miller, 1996, Shaffer and Parks, 1994), including direct competition (Dayton 1985). PSAMP has monitored floating kelp beds (Nereocystis luetkeana and Macrocystis pyrifera) annually (Nearshore Habitat Program, DNR) since 1989 along the Strait of Juan de Fuca and outer coast of Washington, using infrared photos to identify floating canopy area and total surface area of floating kelp beds. However, the extent of kelp canopy visible in aerial surveys, even when done at low tide, depends also on how strong the currents are since blades and floats can submerge completely in strong currents (Britton-Simmons et al. 2008). This finding should be useful in designing future surveys and in interpreting apparent changes over time. Currently, understory (not floating) kelp are not being monitored as extensively. Within the MSA, researchers at the UW FHL and TNC have established transects at several sites in San Juan Channel along which understory kelp cover is being measured annually. One time surveys have also been conducted at some sites within the existing UW MPAs (Britton Simmons, unpublished data). WDNR was recently begun to test underwater videography as a tool for mapping and monitoring subtidal non-floating kelp and other algal communities. Approximately 100 transects are being monitored quarterly around Protection Island using the same equipment that was used for their eelgrass monitoring program. Techniques for characterizing community structure and species composition are being developed. Floating Kelp. According to the Nearshore Habitat Program, floating kelp beds occur along 11 percent of Washington marine shorelines (NHP 2001). They are most abundant in rocky wave and current swept habitats in the Strait of Juan de Fuca, the San Juan Archipelago and along the outer coast, with much lower abundance in central to southern Puget Sound and Hood Canal. The bull kelp, Nereocystis luetkeana (Ind) is the dominant species throughout the Puget Sound region, although the giant kelp Macryocystis pyrifera co-occurs along the Strait of Juan de Fuca

46 and the outer coast (not in the MSA). Floating kelp is one important refuge habitat for juvenile rockfishes (Buckley 1997, Hayden-Spear 2006). Bull kelp is identified as an indicator for rocky subtidal communities in the MSA Plan. Harvesting of sea urchins along the Strait of Juan de Fuca, and probably within the MSA, has been implicated in affecting the kelp canopy area in the Strait of Juan de Fuca (PSAT 2007, PSS 2011). Floating kelp in the Strait increased significantly in total area from 1989 to 2000 (Berry et al. 2005), and there have been increases in many outer coast and Strait shoreline sections (18 of 66 sections) between 1989 and 2004 (DNR data in PSAT 2007, PSS 2011, Fig. 2-3.). Floating kelp has decreased in only one of the easternmost sections in the Strait. Most shoreline sections showed no change over that time period (47 of 66 sections). The reintroduction of sea otters to the Washington coast in 1969-1970 (Lance 2004) may also affect kelp beds as they also remove substantial numbers of urchins. Carter and VanBlaricom (2002) and Carter et al. (2007) studied this potential effect in San Juan Channel by experimentally removing urchins. The overall effect on kelp populations was not evident, possibly due to the generally low urchin densities at these sites or the tendency for red urchins in this region to feed primarily on drift algal material rather than attached algae. Ocean warming, Pacific Decadal Oscillations, and ENSO related changes in temperature and nutrient concentrations may also contribute to year to year variation in kelp beds in this region (PSAT 2007, PSS 2011). So far, sea otters have been observed only occasionally in and near the area of the MSA adjacent to the Strait of Juan de Fuca. Results from an inventory performed by WDNR for the FSJ indicate that ….. (TBA by FDJ acc TM). There has been a significant loss of Nereocystis in the vicinity of the town of Friday Harbor. This can be seen in the aerial photography inventory performed by FSJ. Erin Spencer, in the Marine Algae class, at FHL (Spencer 2006) studied this loss in a class project comparing the historical 1912-15 kelp maps and historical FHL photos to current extent and noted this loss as well. Because losses are seen in areas not covered by docks, the loss may be explained by poor water quality. Understory Kelp. Understory kelp fronds lie on or near the bottom and probably constitute by far the majority of kelp biomass in the MSA. They are present virtually everywhere there are shallow rocky areas, less than 15 m depth, even when floating kelp beds are absent (Webber, 1981). Understory kelp do not show up well in aerial photographs, especially when water clarity is low and they are difficult to distinguish from other types of seaweeds or from seagrasses; they are not good candidates for aerial photographic surveys. The common species within the MSA are Saccharina groenlandica, Laminaria complanata, Saccharina latissima, Saccharina subsimplex, Agarum fimbriatum, and Agarum clathratum, with lesser and local abundances of Pleurophycus gardneri, Costaria costata and Alaria marginata. They often occur in mixed groupings and can be several layers thick, and the species composition varies by depth, wave and current exposure. Kelp beds in the MSA are currently being invaded by a non-kelp floating brown alga, Sargassum muticum, a non-indigenous species that has become quite common in the region (DeWreede 1978, 1980, WA-DNR Shorezone Inventory) and which probably competes directly with understory kelp (Britton-Simmons 2004). Understory kelp are identified as an indicator (Ind) for rocky subtidal communities in the MSA Plan.

47 Within the MSA, understory kelp form the majority of the diet for red sea urchins, Strongylocentrotus franciscanus, as well as supporting other urchins and grazing mollusks, micrograzers, and suspension feeders utilizing kelp detritus (Duggins 1981, Duggins et al. 1990, Duggins and Eckman 1994, Duggins and Eckman 1997, Duggins et al. 1989, 2001). Drift kelp detached from the substrate makes its way to deeper and non-rocky habitats throughout the region and supports populations of sea urchins in habitats that lack much local productivity (Britton-Simmons et al. 2009). As kelp breaks down, decays, and generates small detrital particles, this kelp-derived production may also add substantially to the organic food supply in deep muddy and sandy habitats (Simenstad et al. 1993, Smith et al. 1985), and even to high intertidal zones (Lewis et al. 2007). Waves and currents are very important for kelp growth rate and growth form. The distribution of kelp detritus, and the presence of kelp plants themselves affect many other components of the benthic community (Eckman et al. 1989, 2003, Eckman and Duggins 1991, Duggins et al. 2003). Other marine algae include a broad diversity of brown (Phaeophyta), red (Rhodophyta) and green (Chlorophyta) species for which this region is justly renowned (hundreds of species) (Thom et al. 1976, Andrews 1977, Lindstrom and Foreman 1978, Thom 1980, Harley 2003b, Blanchette et al. 2003, Gabrielson et al. 2006 , ,Menge et al. 2003). Some of the most obvious species are the rockweeds (brown algae) that cover much of the intertidal (Fucus spp.) (Thom 1983, Van Alstyne and Pelletreau 2000, Speidel et al. 2001, Wright et al. 2004, Irvine 2005, Dethier et al. 2005), low intertidal kelp (Pfister 1992a, Van Alstyne et al. 1999ab), the sheetlike green ulvoids (Ulva, Monostroma), some of which exhibit bloom characteristics (Nelson 2000, 2001, Nelson and Lee 2001, Nelson et al. 2003, Van Alstyne et al. 2003, 2007), red Nori (Porphyra spp.), and the difficult to identify, but very diverse, branched red algae and red crustose algae (Dethier 1994, Dethier and Steneck 2001). The diversity of algae increases from the high intertidal zone downward to over -30m MLLW, and many species are distinctly zoned (Bulthuis 1992, for Padilla Bay). Just below the kelp zone (> 15m), foliose red algae and pink coralline algae (also reds) often dominate space on rock surfaces, before petering out due to lack of light and being replaced by encrusting invertebrates in the deepest zones. The rock surface underneath understory kelp is also a prime habitat for these smaller and diverse algae (Hodgson and Waaland 1979, Garbary et al. 1999, Wyllie- Echeverria et al. 2004b). In general, these species are frequently collected and described, but they are difficult to quantify in the field so true estimates of their abundance are lacking for most sites.(see comment above about Protection Island. Recent surveys as part of the Smith-Minor Island Marine Reserve at Partridge Bank, Smith Island, and Protection I are beginning to be put into context with the over 100 years of algal dredging done from the FHL so the deeper subtidal algal communities are beginning to be better understood at least in terms of distribution and biodiversity. They are also important components of the food web, and can be the main primary producers in rocky habitats lacking kelp. In soft bottom habitats, benthic productivity is dominated by microalgae (e.g. diatoms) on the sediment surface. b. Seagrasses (MSA Target: Nearshore mud, sand and gravel communities) Globally, seagrasses provide valuable ecological services, including nursery habitat and sediment stabilization. In the nearshore environment they are sensitive indicators of local and broad scale ecosystem change (reviewed in Kenworthy 2006, Wyllie-Echeverria et al. 2006). Therefore

48 monitoring changes to plant distribution and density provides important information related to the carrying capacity of a particular ecosystem to support species dependent on seagrass cover such as juvenile fish, invertebrates and waterfowl in the MSA and the broader region (Phillips 1984). In addition, because these plants rapidly respond to adverse water quality conditions, such as increased turbidity or eutrophication, they provide an early indicator of events that may have broad ecosystem impact (Neckles 1994).

These characteristics of seagrasses motivated The Washington State Department of Natural Resources (WDNR) to select eelgrass Zostera marina, ubiquitous throughout Washington State (Phillips 1984), as an indicator of ecosystem condition in the greater Puget Sound (Berry et al. 2003). Elements of the WDNR monitoring program included the computation of abundance estimates and the upper and lower limits of growth along the tidal gradient. Results of this monitoring program, launched in 2000, indicate that while the sound wide estimates of abundance have remained relatively constant, there is evidence that site level decline is common throughout the region (Gaeckle et al. 2007). For studies of seagrasses in the PSR, see: (Thom 1988, 1990, Williams and Ruckelshaus 1993, Ruckelshaus 1995, Nelson 1997, Nelson and Waaland 1997, Van Mooy et al. 2002, Dumbauld and Wyllie-Echeverria 2003, Wyllie- Echeverria et al. 2003ab, Haugerud et al. 2004, Hughes and Wyllie-Echeverria 2007, Rearick et al. 2007).

Seagrass species respond relatively quickly to environmental change at local and regional scales. For example, an overwater structure that does not allow sunlight to reach the seafloor, excessively hot or cold temperatures (or both) in the lower intertidal region or disease can result in reduction or elimination of seagrass cover in one growing season. Conversely, an increase in local or regional water clarity can bring about population expansion. Monitoring the distribution and density of seagrass species can provide a signal to noise ratio that enhances prediction of overall ecosystem health (Norris et al. 1997). There are caveats though, and it is recognized that variation in seagrass stem density or bottom cover, while potential indicators of the direction of change, are not reliable predictors of population collapse. To fine-tune predictive ability, molecular ecology, biochemical analysis, and pathology techniques are being considered as important elements in seagrass monitoring programs (Watabayashi et al. 2002). Existing Monitoring. WDNR has been monitoring the status and trends of eelgrass (Z. marina) since 2000 and the program is ongoing. The Subtidal Vegetation Monitoring Program (SVMP) tracks changes in the total area and depth distribution of eelgrass at three spatial scales (sites, regions, and Puget Sound). To meet these goals, it uses a statistical framework to randomly sample all potential eelgrass habitat within Puget Sound and extrapolate results over multiple spatial scales with known confidence limits. Reports and data are available at: http://www.dnr.wa.gov/ResearchScience/Topics/AquaticHabitats/Pages/aqr_nrsh_eelgrass_moni toring.aspx In the wake of the dramatic and sudden loss of eelgrass in small embayments throughout the San Juans (PSAT 2007, PSS 2011), but particularly in Westcott Bay, two investigations were initiated. The Friday Harbor Laboratories (FHL), UW, Friends of the San Juans, and the United States Geological Survey, Pacific Science Center, Santa Cruz collaborated to initiate a monitoring program at several sites (See Appendix 4 for location) in 2005. Collaboration between FHL and USGS in this program continues. In addition, FHL also began to monitor two other seagrass species, Phyllospadix scouleri and Zostera japonica, (Harrison and Bigley 1982),

49 in 2005 and 2006 respectfully. Monitoring metrics include sterile and flowering stem density, rhizome internode length, canopy height and disease diagnosis of leaf material. Estimates of genetic diversity between sites and clonal diversity within a site are underway with Z. marina and P. scouleri and biochemical analysis of Z. marina below ground tissue will be initiated in a pilot program at three sites in summer 2008. Water quality in eelgrass habitat has also been investigated recently (Kull et al. 2007). Also, WDNR has started its Eelgrass Stressor-Response Project. Monitoring Programs conducted by WDNR and UW have documented severe eelgrass losses in the San Juan Islands and at several sites in Hood Canal, but the causes are not yet known. This project is investigating these causes and supports efforts to restore eelgrass beds and the ecological functions they provide – sediment stabilization, improvement of water clarity, and provision of complex habitat that increases biodiversity and in particular supports at-risk species. An interdisciplinary team of state, federal and university scientists is conducting field experiments, intensive monitoring, laboratory analysis and modeling to address the research questions. A conceptual model provides the structure for the project activities and this model will be adapted based on project results. The project approach measures the ecological response of native and transplanted eelgrass in sites with contrasting environmental conditions: e.g., Wescott Bay/Mosquito Pass (high/low turbidity) and upper/lower Hood Canal (high/low dissolved oxygen). Water quality sensors are deployed at fixed locations. Water column and sediment porewater samples are collected for nutrient analysis. Sediment geochemisty (redox potential, sulfide levels) are characterized in collected cores. Current meters characterize hydrodynamic regimes. (Schanz, A., et al. 2009, Identifying eelgrass (Zostera marina L.) stressors in Puget Sound, Washington (USA) - A case study in the San Juan Island Archipelago, in the Proceedings of the 2009 Puget Sound Georgia Basin Ecosystem Conference (new reference TBAxxx). In Westcott Bay, a study of intertidal communities of the muddy shorelines found that losses in eelgrass in this bay were not paralleled (over the same period) by changes in the abundances or diversity of clams, worms, and other species in the tide flats. This implies that the dramatic loss of eelgrass was caused by some factor uniquely damaging to that plant rather than to the whole ecosystem (Dethier and Berry 2008).

Proposed Monitoring. It is well established that a reduction in the distribution and density of local, regional, and potentially hemispheric seagrass populations forecast a decline in overall ecosystem health in estuarine and coastal systems. It is also recognized that monitoring changes in abundance (e.g. stem density) is not sufficient to predict population collapse or increase (Hemminga and Duarte 2000). Ongoing investigations in the San Juan Archipelago suggest that in addition to monitoring stem density a rigorous monitoring program should also characterize population sub-structuring and site-specific clonal diversity patterns to understand the impact of natural and anthropogenic disturbance events on the health and resilience of seagrass flora at local and regional scales. This approach is supported by other studies on the West Coast of North America (e.g. Muñiz-Salazar 2006).

Tracking the success of sexual reproduction from fertilization to seed viability and the capacity of rhizomes (buried stems that function as storage organs) to store energy for fall and winter growth, can reveal yearly variation in distribution and density patterns. Fertilization and seed

50 viability rates can be determined through microscopic evaluation of floral development and seed staining procedures in the laboratory (Wyllie-Echeverria and Alphin in prep). Rhizome efficiency is evaluated using chemical techniques to determine proximate constituents within tissue samples (Dawes 1998). Sexual reproduction and rhizome storage are controlled by environmental conditions with primary regulation through temperature, light, and water motion. Recent advances in the development of remotely operated sensors to track environmental conditions makes it possible to relate change in floral development and/or rhizome efficiency to site conditions. If stem density, floral development and rhizome efficiency are to be used as predictors, then environmental conditions must also be monitored. d. Salt Marshes Although there are extensive salt marshes on the nearby mainland (e.g. Padilla Bay, DePhelps 1996), salt marshes within the MSA are very limited in extent. Salt marshes are dominated by grasses and other plants of terrestrial origin, which are adapted to regular immersion in seawater, and exposure to air during tidal cycles (Eilers et al. 1982,1984, Ewing 1983, 1984, Thom and Hallum 1991, Thom 1992, Heatwole and Simenstad 2004). Salt marshes provide unique habitat for particular benthic marine species, as well as for insects and birds (Smith 1976, Kentula 1986, Williams and Hamilton 1995). Invasion by the cordgrass (Spartina anglica, S. alterniflora) has been documented at many sites along the west coast, including Washington (Dumbauld 1995, Stiller and Denton 1995, Kilbride and Paveglio 2001, Hacker et al. 2001, 2004, Hellquist et al. 2002, Hahn 2003, Hedge et al. 2003, Holsman and McDonald 2004, Reeder and Hacker 2004,) and efforts to remove it have been locally successful (Argyle Lagoon) At sites in Washington, it may take over areas that would otherwise be occupied by intertidal clam populations. Existing monitoring. The Puget Sound Nearshore Ecosystem Restoration Program has mapped changes in the nearshore marine environment, including salt marshes, comparing historical maps (T-sheets from 1850-1890) to current conditions. Proposed monitoring. Though limited in areal extent, it would be a serious mistake to overlook these habitats. They are often subject to development (fill) Their importance (as “pocket estuaries”) in salmon/Chinook juvenile rearing is being recognized as very important (see the Skagit Coop studies). Mapping and monitoring is pretty straightforward, including aerial photography plus extensive groundtruthing. Classification schemes have been developed by the Natural Heritage program and TNC. (See http://www.dnr.wa.gov/ResearchScience/Topics/NaturalHeritage/Pages/amp_nh.aspx).. Another marine vegetation type not covered in this document are spit-berm vegetation (See Dethier 1990). These are widespread in their abundance in the MSA. They include the vegetation communities found in log lines, on gravel spits, seagrass backshores, etc. See recent work by FSJ, SJC Planning Department, and Lead Entities for mapping of these habitats. e. Brackish water habitats Because of the lack of large rivers in the MSA, the extent of brackish water habitat is not large. Most embayments are marine in character, although surface salinity can be reduced seasonally from Fraser River outflow, especially in the northern part of the MSA. The southernmost tips of

51 the islands are strongly affected by the Straits of Juan de Fuca and thus see fewer instances of reduced salinity. True brackish water habitats are limited to enclosed lagoonal habitats with streams emptying into them, and intertidal habitats with freshwater input (Tanner et al. 2002). The fauna and flora of brackish water habitats has not been quantified within the MSA. Note: Wetland area coverage is defined as an indicator in the MSA Plan, for the nearshore mud, sand and gravel communities target. (No existing and proposed monitoring)

2.5 Intertidal Habitats and Biotic Communities The intertidal zone is the region between the highest and lowest points along the shoreline marked by the tides, and thus intertidal habitats experience both aerial and aquatic conditions regularly. Across the Puget Sound Region, intertidal species diversity generally increases from south to north (, Dethier & Schoch 2005 Dethier 2007) for soft substrates, however the mechanism behind this trend is unknown. This MSA has a high diversity of rocky intertidal habitats. It ranges from moderately exposed totally marine area such as Cattle Point and Iceberg Point, to highly protected more estuarine areas such as those along San Juan Channel, on several islands.

Rocky Intertidal Communities (MSA Target) Rocky intertidal communities are characterized by distinct zonation, going from lichen and cyanobacterial assemblages in the highest reaches (splash zone) to barnacles (Dayton 1971, Sebens and Lewis 1985) and algal assemblages in the high to mid intertidal, and subtidal species at their upper limits in the lowest zone. Mussel beds, characteristic of many west coast intertidal communities (Paine 1976, 1992, 2002, Paine and Levin 1981, Suchanek 1981, Seed 2000), are rare in the MSA (Dayton 1971). A few beds of the large California mussel (Mytilus californianus) can be found on the most wave exposed southwestern shores, and scattered individuals and small clumps of other Mytilus species occur throughout the MSA. Seastars (Pisaster ochraceus, Leptasterias hexactis) are important predators in the intertidal zone (Menge 1972ab, Menge et al. 1994), as are certain birds (e.g. oystercatchers) and mammals (raccoons, mink). Herbivorous mollusks can be very abundant (e.g. chitons, snails) and can determine the extent and species composition of their algal prey (Dethier and Duggins 1984, 1988, Duggins and Dethier 1985). Large beds of sea anemones (Sebens 1981, 1982, 1983) are also common on more exposed rocky shores. Extensive surveys of rocky intertidal communities in the MSA and nearby regions were conducted by Nyblade (1979). See also: (Wootton 1991, 1995, 2002, Wieters and Navarette 1998, Connolly 1999, Harley 2002, 2003a, Jenkins et al. 2002, Paine and Trimble 2004, Freidenburg et al. 2007).

Compared to other parts of the northeast Pacific, rocky intertidal communities in this region are particularly susceptible to temperature and desiccation effects because extreme summer low tides occur in the middle of the day when solar radiation is strongest (Dayton 1971, Helmuth et al. 2006). Dayton (1971) recognized that the intertidal zone in the San Juan Archipelago did not support the high biomass characteristic of the exposed outer coast, probably because of severe physiological stress combined with the lack of wave splash. Increased temperatures associated with climate change is likely to make life in the intertidal zone more stressful here than in other

52 parts of the Pacific Northwest. Intertidal communities are also subject to severe damage from oil spills, which float on water and end up coating intertidal rock, sand, and organisms that live there, often with devastating effects. Oysters are important members of rocky intertidal communities; in the MSA; at a few sites the invasive (but economically important) Asian oyster, Crassostrea gigas, has replaced native oysters and other intertidal species (e.g. Fucus) (Klinger et al. 2006). Olympia oysters are only known to inhabit Shoal Bay on Lopez Island (Betsy Peabody, pers. comm.). In earlier reintroductions, all seeded populations died within two to three years because river otters ate the reintroduced individuals (Russel Barsh, pers. comm.). The conservation focus has shifted from reintroduction to enhancement (Betsy Peabody, personal communication) and they are also aquacultured in several locations in the Puget Sound Region, including Lopez Island. Crassostrea gigas is the main oyster used for aquaculture in the state, and many sites have been dedicated to production of this species (Burnett and Milardo 2000, Dumbauld et al. 2000a, Dumbauld et al. 2001a, Dumbauld 2002).

Soft Substrate Intertidal Communities (MSA Target: nearshore sand, mud and gravel communities). Soft (Unconsolidated) substrates are common in the MSA, and throughout the Puget Sound Region (S Dethier & Schoch 2005, Dethier and Berry, 2008, 2009. They are important habitats for juvenile fish, they support eelgrass beds under some conditions, and they are important foraging habitat for many species of bottom fish and for shorebirds. There is a distinct, though hard to see, vertical zonation of infaunal species with tidal height, and also within the sediment. Surficial species may be highly mobile, and sometimes ingest or disturb the sediment surface. Infaunal polychaete worms include those that travel through the sediment as well as those that establish more or less permanent tubes, thus giving the sediment substantial structure. Bivalve mollusks, primarily clams, also establish shallow to deep burrows depending on the species and the sediment type. Deeper layers within the sediment become anoxic, producing the characteristic black layer often with a strong smell of hydrogen sulfide. This redox (discontinuity) layer limits the depth that many species can live, but provides a resource for certain bacteria that can gain energy from oxidizing reduced sulfur compounds. Within the MSA, there are many examples of shallow embayments with these communities, including the spectacular and extensive tidal flats of False Bay on San Juan Island, a marine protected area owned by the University of Washington. This has been the site of numerous published studies of individual species biology and community ecology (Nichols 1972, Sibert et al. 1979, Brenchley 1981, Carroll and Wethey 1990, Wilson 1991, Simenstad et al. 2003).

Existing Monitoring (All Intertidal Types). Whole community monitoring efforts in the San Juan Archipelago are limited. Megan Dethier (UW FHL) has assessed percent cover and counted the number of mobile individuals of all species present within 30 quadrats in the rocky intertidal zone on San Juan Island annually since 1989 (M. Dethier, personal communication), at two sites (Cattle Pt., Reuben Tarte Park) as part of UW classes. Dethier similarly has assessed biota on rocky shores and in soft-sediments, including clam abundances, at numerous sites on San Juan Island since the 1990s (including in San Juan Island National Historical Park). The Marine Conservation class at FHL began a set of intertidal quadrats in summer 2007. Rocky

53 intertidal species richness (Ind) is defined as an indicator for the MSA target. Height and width of intertidal zones are also indicators, as are abundance of limpets, barnacles and rockweeds (Fucus). The air and water temperature regime is also identified as an indicator (Ind).

Intertidal clams in the San Juan archipelago (native clams, Ind) are monitored by WDFW by three types of surveys: creel surveys, effort surveys, and abundance estimates (Jenny Whitney WDFW, personal communication). Since 1987 annual creel surveys have occurred at English Camp and Spencer Spit and entail asking diggers how many of each species of clam were harvested. Effort surveys are conducted by flying above the shoreline at Spencer Spit, English Camp, and Mud Bay and counting the number of people on the beach at low tide. Effort surveys began in 1984 and occur on a monthly basis between April and August. These data are then extrapolated into total harvest counts based upon the creel and effort survey data.

Abundance estimates of the clam populations began in 1998 and are conducted annually at English Camp and Spencer Spit by extracting clams along transects. WDFW has found that native littleneck clams have declined and invasive varnish clams have increased at Spencer Spit, consistent with trends for these species from California to Alaska. Mechanisms for these population shifts remain unknown. The UW FHL K-12 Program have assessed clam populations at Argyle Lagoon beach annually since 1999 under supervision of FHL scientists and UW students (D. Duggins, M. Dethier and colleagues, FHL, SJI public schools).

Whole-community sampling has not been conducted on a regular basis within the MSA, although there have been one-time surveys at a number of sites. The physical and chemical conditions of nearshore sand, mud and gravel communities are also identified as indicators for this MSA target. These include depth of the anoxic horizon in embayments, ammonia in sediments, and dissolved oxygen concentration in the water column (Ind). Sediment grain size in embayments (Ind), and a productive supply of sediment for beaches (Ind) are also identified as indicators for this target. Megan Dethier has been developing and using a technique for characterizing intertidal unconsolidated substrate infauna. See: http://www.dnr.wa.gov/ResearchScience/Topics/AquaticHabitats/Pages/aqr_nrsh_biotic_commu nity_monitoring.aspx

Proposed Monitoring. We suggest maintaining the UW FHL rocky intertidal sampling at Reuben Tarte and Cattle Point sites; a site at Cantilever Point (as close as possible to Nyblade’s 1970s site) was also added in 2007 and will be continued. It would also be helpful to add sites at Cedar Rock and Pt. George on Shaw Is., Argyle Lagoon and False Bay to the UW efforts, since these are all Biological Preserves owned and maintained by UW. SJC could partner with FHL and the NPS to establish or maintain sites at American Camp and English Camp (intertidal monitoring programs were set up in these Park areas by Dethier and maintained for several years by Park staff, then discontinued). New intertidal monitoring sites should be established on all the major islands, including rocky shores and soft sediment beaches or mudflats. In addition to sampling the biotic communities, an effort should also be made to collect and archive frozen sediment samples to document hydrocarbons and other contaminants in these sediments prior to an oil spill or other contamination. Sites should be selected such that there are a reasonable number along the path

54 of tankers carrying oil and petroleum products, but should also be chosen to represent the various habitat types and regions within the MSA. This is a good opportunity for citizen monitoring since the major groups of rocky shore plants and animals can be taught to volunteers and they can survey sites using simple quadrat methods. Soft substrate methods are more difficult (Dethier and Schoch 2005) and will probably limit the number of sites chosen. For intertidal survey methods see: Dethier et al. 1993, Zacharias et al. 1998, 1999, Ferdana 2002, Emmett et al. 2004, Ferraro and Cole 2004, Garono et al. 2004, Jamieson and Smiley 2004, Dethier and Schoch 2006, Murray et al. 2006.

2.6. Subtidal Habitats and Their Biota

Subtidal habitats comprise most of the MSA; they include everything from flat muddy bottoms to vertical rock surfaces, giant sand waves, and mixed substrata. Compared to the very limited area of intertidal habitats, subtidal habitats are extensive in area and harbor a large biomass of animals and plants. The shallow subtidal zone is especially productive due to the abundance of kelp and other primary producers (other macroalgae, seagrass), and this productivity is exported to both intertidal and deeper subtidal habitats, providing food for large populations of invertebrates and their predators, including fish. Subtidal surveys in the MSA and in adjacent waters include: (Lie and Evans 1973, Bernard 1978, Webber 1979, Levings et al. 1983, Luternauer et al. 1983, Guenette 1996, Moran 1999, Copping and Mark 2004, Thuringer et al. 2004, Woodruff et al. 2004, (recreational diver surveys). Rocky Subtidal Communities (MSA Target). Characteristic rocky subtidal assemblages can be found on rock surfaces, including kelp and smaller algae on horizontal and sloping rock in shallow areas, and diverse marine invertebrates on vertical and steeply sloping rock as well as on horizontal rock in deeper habitats (> 15 m). These invertebrate communities are composed of sea anemones, sponges, sea squirts, barnacles, mussels, and hundreds of other species (Young and Chia 1982, Young 1985, 1986). Harvested resources from these habitats include kelp, sea urchins, crabs, sea cucumbers, and many species of bottom fish. Artificial reefs have been constructed in some locations (Hueckel et al. 1989), but are generally not appropriate in sites that already contain substantial hard bottom.

Soft Substrate Subtidal Communities (Target: nearshore sand, mud and gravel) Muddy and sandy areas have varied assemblages of invertebrates, and few macroalgae, although shallow sediments are often coated with layers of diatoms and other microalgae. The physical and chemical conditions of nearshore sand, mud and gravel communities are also identified as indicators for this MSA target. These include depth of the anoxic horizon in embayments, ammonia in sediments, and dissolved oxygen concentration in the water column (Ind). Grain size in embayments (Ind), and a productive supply of sediment for beaches (Ind) are also identified as indicators for this target. Biotic community structure varies greatly with grain size, water flow, and level of bioturbation in soft sediment communities (Smith 1981, Gallagher et al. 1983, Iribarne et al. 1992, Zardus 1995). Another soft substrate subtidal habitat is coarse sand, sometimes occurring as sand waves. There are several extensive fields of sand waves in the MSA, recently identified as important sand lance habitat (G. Greene, pers. comm.).

Existing Monitoring. Existing monitoring consists of rocky bottom transects (50 sampling locations) maintained by UW FHL (K. Sebens) since 2006 in the Pt. Caution/Colin’s Cove area of the UW FHL Preserve (entire biotic community). Another set of subtidal transects has been established at Yellow Island and adjacent islands and was sampled in 2006 to 2008 (M. Dethier, UW FHL). WDFW monitors fish populations at these sites and at Pt. George on Shaw Island, within the established MPAs. Citizen volunteers (REEF) (www.reef.org) conduct SCUBA surveys of some of the large common invertebrates and fish at over 50 sites in the MPA (not monitored over time). Other subtidal monitoring protocols combine a rapid field assessment, and substantial taxonomic lumping, with extensive collections that can provide accurate species identification later (e.g. NAGISA, http://www.coml.org/descrip/nagisa.htm).

Proposed Monitoring. We suggest maintaining the UW FHL sampling at the Pt. Caution/ Colins Cove sites. It would also be helpful to add sites at Cedar Rock and Pt. George on Shaw Is., near Argyle Lagoon, and outside False Bay to the UW efforts since these are all Biological Preserves owned and maintained by the UW. To provide a complete census of the region, subtidal monitoring sites should be established at rocky shores and soft sediment habitats of all major islands, especially outside protected marine areas where monitoring sites don’t currently exist. We also suggest a broad-scale survey of subtidal habitats, similar to that done for intertidal habitats throughout Puget Sound (Dethier and Schoch 2005) within the MSA, to establish species presence and map habitat types. This could be done in conjunction with other monitoring efforts such as mapping rockfish habitat. Subtidal monitoring can be broken down into bathymetry, geological and substrate type mapping, as well as biotic community mapping or characterization. The biotic component often is derived from the underlying geology/depth. The study needs a good basemap- which can be assembled from work done by Gary Greene and others, and this should be a high priority. Seafloor mapping has been addressed as a high priority action item by the West Coast Governors Agreement on Ocean Health.

Citizen science has a good track record with subtidal surveys (Copping and Mark 2004), because trained SCUBA divers volunteer to describe subtidal habitats and organisms. Locally, REEF (www.reef.org) is an excellent example, a group that works with the SeaDoc Society (Joe Gaydos) to quantify common subtidal species in the Pacific Northwest. REEF surveys include over 50 sites in the MSA. a. Sea Urchins Four species of sea urchins (Ind) inhabit the San Juan archipelago, with two of these commercially harvested: red (Stronglyocentrotus franciscanus) and green (S. droebachiensis) urchins. The purple urchin, (S. purpuratus) is common on the outer coast and rare in the MSA, and the fourth species is a deep-water urchin (S. pallidus) common at some sites in the MSA. Index stations surveyed by WDFW in 1995, 2005, and 2007 indicate that the red sea urchin population is stable (Bradbury 1991, PSAMP 2007). WDFW also attempted to monitor the green sea urchin abundances but discovered that green sea urchins were too mobile to monitor

56 with static index stations. Landings of green sea urchins indicate that current harvest levels are controlled and sustainable (Michael Urlich pers. comm.). The San Juan Channel region is closed to urchin harvesting at present, since 199XX. b. Sea Cucumbers The red sea cucumber (Parastichopus californicus) (Ind) occupies a wide range of habitats from deep to shallow, muddy to rocky areas. Despite commercial harvest, no monitoring programs exist for red sea cucumbers because their mobility renders current monitoring methodology (use of stationary index stations) ineffective. Current harvest quantities are considered conservative and sustainable by WDFW, although no data exist to substantiate or refute this claim. There are several other sea cucumber species in the MSA, one of which (Cucumaria lubrica XXX) forms extensive subtidal beds, and is a common prey species for other invertebrates such as seastars (Mauzey et al. 1968, Rodgers and Bingham 1976). c. Pinto Abalone Pinto abalone (Haliotis kamtschatkana) inhabits rocky substrates, often near kelp beds. Although these herbivores have never been commercially harvested in Washington, dramatic declines due to legal and illegal harvest by divers during the last twenty or more years across their range (Rothaus et al. 2003) have resulted in pinto abalone being listed as a species of concern by the U.S. National Marine Fisheries Service, listed as threatened by the Committee On the Status of Endangered Wildlife In Canada, and listed as endangered by IUCN. There was a sport fishery on this species until 1994.

A monitoring program lead by WDFW at ten index stations across the San Juan archipelago found dramatic declines between 1992 and 2005 (Ref XXXX). This program also found a shift in the size (age) structure of pinto abalone, with increasing frequency of larger (older) animals, suggesting a decline in recruitment. A total of 66 recruitment modules (stacks of tiles with spaces between) have been placed at three sites with known abalone populations and studied between spring of 2005 and fall of 2007 (Don Rothaus, pers. comm.); data from this study indicate recruitment is minimal to nonexistent, and thus populations may not be sustainable. This species maintains more viable populations in Canada. Rising seawater temperatures, and ocean acidification, will further challenge this northern, cold-adapted, species. Efforts to enhance local populations, and to increase density at selected sites, are underway (Straus et al. 2005) and may provide a means to rehabilitate populations in this region (WDFW). d. Crabs and Shrimp WDFW has monitored commercial crab harvest since the 1970s using fish tickets filled out by harvesters (Williams 1979). Beginning in 1995, WDFW annually samples the abundance and shell condition of tanner (Chionoecetes spp.), Dungeness (Cancer magister), and red rock crabs (Cancer productus) at standard crab plots (Don Velasquez, pers. comm.), some of which occur within the MSA. The crab fauna of the MSA is diverse and includes important and common species that are not harvested, including the kelp crabs (Baldwin et al 1992), and others. Dungeness crab are important predators on other benthic species (Stevens et al. 1982, 1984).

57 Harvest increased from 1995-2005 by about 25% (PSAT 2007, PSS 2011). Dungeness crab recruitment and habitat use have been investigated at a number of sites on the outer coast (Armstrong and Gunderson 1988, Dumbauld et al. 1988, 1993, 1998, 2000b, McGraw et al. 1991, Fernandez et al. 1993ab, 1994, Iribarne et al. 1994ab, 1995, Eggleston and Armstrong 1995, Eggleston et al. 1998, Banks and Dinnel 2000, Warner and Visser 2000, Armstrong et al. 2003, Holsman et al. 2003ab, 2006, Visser et al. 2004,), and in the PSR (McMillan et al. 1988ab, 1995, Dinnel et al. 1989, 1993). For shrimp, abundances and sex ratios are monitored at 10 locations within Griffin Bay and Iceberg Point by WDFW twice annually (WDFW, unpub. Data). For invasive crab species (e.g. green crabs) see Section 5.11 e. Other invertebrates Recent investigations have provided evidence of extensive glass sponge populations on deep rocky reefs within the MSA, particularly along the west side of San Juan Island and south of San Juan and Lopez Islands (R. Johnson, pers. comm.). These deep water sponges are fragile and are threatened by bottom trawling and by changing environmental conditions. While these species have been collected in the past (e.g. specimens in FHL collections), the extent of their populations has not been determined and should be a focus of future monitoring and mapping. The MSA, and the Salish Sea, are also home to populations of the world’s largest octopus (Octopus dofleini, Hartwick et al. 1984), as well as several other cephalopod species.

2.7 Fish a. Groundfish Demersal fish species, also known as groundfish live close to or on the bottom as juveniles and adults. There are over 150 groundfish species in the Salish Sea. Many of these species have been fished in past decades, with some populations declined since the 1970s. Species that have declined include Pacific cod (Gadus macrocephalus), Pacific hake (Merluccius productus), walleye Pollock (Theragra chalcogramma), spiny dogfish (Squalus acanthias), and several rockfish species (Sebastes spp.) (PSAT 2007, PSS 2011, Figs. 2-23 to 2-29). The severe decline in groundfish throughout the Puget Sound Region (PSAT 2007, PSS 2011, Fig. 2-31) has probably affected the rest of the food web. It has been suggested that removal of large numbers of predatory fish (e.g. cod, dogfish) in the Puget Sound region may have reduced predation pressure oncrabs, ratfish, flatfishes and possibly other invertebrates, which allowed their populations to increase (PSAT 2007, PSS 2011). The status of Puget Sound region groundfish has been reported in Kuons and Cardwell (1981), Palsson et al. (1997), PSAT 2000, PSAT 2002, PSAT 2007, PSS 2011.

Rockfish, Lingcod and Greenling (MSA Target)

A broad discussion of groundfish stocks in the Puget Sound Region is available in the 2007 Puget Sound Update (PSAT 2007, PSS 2011), which includes WDFW data on several rockfish

58 species. This region contains at least 27 species of rockfish, ten of which were common targets of recreational fishing. Data are available only for copper (Sebastes caurinus ) and quillback (Sebastes maliger) rockfish, showing that spawning potential has dropped to about a quarter of that in the 1970s (PSAT 2007, PSS 2011, Figs. 2-27 to 2-29). Rockfish are long-lived, slow growing, and slow to recruit. Populations have not yet recovered from decades of harvest, even though increasingly stringent limits have been placed on catches of rockfishes over the past two decades. In 2010, three species of rockfish were listed as endangered (bocaccio rockfish, Sebastes paucispinis) or threatened (canary rockfish, Sebastes pinniger, yelloweye rockfish, Sebastes ruberrimus) and were thus afforded additional protection. For further information, see: http://www.nwr.noaa.gov/Other-Marine-Species/Puget-Sound-Marine-Fishes/ESA-PS-Rockfish.cfm

The lingcod (Ophiodon elongatus) population collapsed before the 1970s in the south Sound, and in north Sound during the 1980s. Both areas have shown strong recovery since stricter harvest or catch limits were imposed, including a five-year moratorium in the south sound (PSAT 2007, PSS 2011, Fig 2-30). In the MSA, lingcod are larger and more abundant in MPAs than outside, where they feed on a variety of forage fish, shrimp, salmonids and some rockfish (Beaudreau and Essington 2007).

Greenling (Family Hexagrammidae) are often the most common groundfish species in shallow rocky subtidal areas in the MSA. Their populations are currently recovering from decades of harvest. Their status is considered “average” in south Sound, and “unknown” in north Sound (and the MSA) according to WDFW (PSAT 2007, PSS 2011, Table 2-3). Monitored flatfish have been increasing in the region closest to the MSA, with English sole (Parophrys vetulus) biomass showing the highest gain (PSAT 2007, PSS 2011).

This MSA Plan target identifies several indicators (Ind) including: areal coverage of rocky habitat, juvenile rockfish refuge (understory kelp, floating kelp rafts), population size (based on harvest records, in situ surveys), spawning potential (age structure of selected species), and sufficient recruitment (young of the year).

Existing Monitoring. WDFW’s comprehensive review “The Biology and Assessment of Rockfishes in Puget Sound” became available in late summer 2009. This report reviews the distribution, life history, and status of 28 species of rockfish in the greater Puget Sound area, 20 of which have been found in the San Juan archipelago. In general, rockfishes occur in benthic rocky reef habitats and in open water. Monitoring of occurrence and abundance occurs through trawl, video, and SCUBA surveys.

Focused studies by Eric Eisenhardt in the San Juan Islands document the abundance of rockfishes in regulatory marine reserves compared to nearby reference sites (Eisenhardt 2001) and similar comparisons for voluntary bottomfish recovery zones (2007) (Eisenhardt 2007, MRC report). Since 2004, WDFW has instituted systematic monitoring of rockfish harvest including estimates of both retained and discarded catch. Previously, recreational harvest estimates were only conducted in conjunction with sampling of salmon catch and were not available during periods when salmon fisheries were closed. Some data on rockfish abundance at transects in and outside of marine reserves near Yellow Island were conducted in 2005-8. Numbers are highly

59 variable in space and time, making it difficult to assess recovery in protected areas, although the data suggest that populations in protected areas may be increasing.

Proposed Monitoring. Because the MSA plan hypothesizes that further regulation of fishing mortality is necessary for the recovery of rockfish abundances and length distributions, close monitoring of these populations will be important. Abundance and length distribution assessments in regulatory, voluntary, and open areas should be continued on a regular basis to test hypotheses about the efficacy of harvest controls. Monitoring in MPAs and nearby control sites is being conducted by MWRA on a regular basis (W. Palsson, Pers. Comm.), including MPAs south of the SJC MSA. Continued monitoring of rockfish in the voluntary non-take areas has been funded by the MRC and by the SeaDoc Society. We proposed regular monitoring of a broader range of sites as part of the MSA plan, funded by SJC through the MRC. A one-time assessment of all suitable rockfish habitat in the San Juans will provide valuable information affecting the design of future monitoring plans as well as the MRC’s adaptive management of the current bottomfish recovery program. b. Pelagic fish: Forage fish (MSA Targets: Pacific Salmon, Seabirds) Pacific herring (Clupea pallasi), surf smelt (Hypomesus pretiosus), and Pacific sand lance (Ammodytes hexapterus) (Ind) are grouped in a category called forage fish as they are prey species for fish, avian, and mammal apex predators. These fish species utilize intertidal or subtidal benthic substrates for spawn deposition and incubation (Pentila 1997, Quinn 1999). Because of this obligate relationship with shoreline habitats, forage fish species are at risk from development activities. Forage fish play a key role in marine food webs, connecting plankton and the wide range of larger predators, including fish, seabirds and marine mammals.

Surf smelt and Pacific sand lance spawn on the upper third of sand/gravel beaches. Pacific herring spawn in lower intertidal and shallow subtidal habitats on submerged aquatic vegetation. Surf smelt spawning activity has been documented year round in San Juan County. Pacific sand lance spawn from November through February. Pacific herring spawn in San Juan County from late January through April. Larval abundance of surf smelt, herring, sand lance, and juvenile herring (Ind), are also identified as indicators for the Pacific salmon MSA target. Adult abundances are indicators (Ind) for the seabird target.

Existing Monitoring: Surf smelt and Pacific sand lance. The San Juan County Forage Fish Project (FSJ 2004) conducted comprehensive county-wide surveys for surf smelt and Pacific sand lance spawning from 2000- 2003. Aerial photo analysis with follow-up field verification at a subset of sites identified over 600 beaches (roughly 80 miles) of potential spawning habitat in San Juan County (Moulton and Pentila 2001). Between July 2001 and December 2003, 1251 bulk samples and forage fish field surveys were collected using WDFW protocols (Pentilla 2001) from 538 sites on 24 islands. This coverage represents 91% of potential spawning habitat in San Juan County. Nine percent of potential spawning sites were not sampled because of: existing protected status (e.g. total length in preservation lands), physical access, time constraints, or a lack of landowner permission (only 17 sites out of 590 potential spawning beaches were not sampled due to denied access).

Of the sampled sites, 254 (47%) were sampled once and 284 (53%) were sampled a minimum of two (and up to 11) times. At each survey site with suitable potential habitat, a substrate sample was collected to determine evidence of spawn. Additional information on nearshore habitat variables was also recorded during field surveys. Variables recorded at each station included: latitude/longitude; tidal elevation; coded entries for beach substrate type; sample transect elevation; shade; spawn evidence and density; spawn incubation habitat width; potential spawn habitat length; and upland conditions. The presence of docks, eelgrass beds, seawalls, freshwater influence, outflow pipes, boat ramps, and other major beach features were also recorded. A digital photograph of the sample beach, with a latitude/longitude and date/time recorded on every photo, was taken with each sample.

In surveys conducted in San Juan County from 1989 to 1999, Washington Department of Fish and Wildlife (WDFW) documented 14 surf smelt and eight Pacific sand lance spawning sites (Pentila 1999). The San Juan County Forage Fish Project documented presence of surf smelt or sand lance spawn at 50 beaches in San Juan County, 39 (62%) of which were previously undocumented spawning sites. Coupled with the historic WDFW data, 63 discrete spawning locations are documented for San Juan County, representing 11% of potential spawning sites and 16% of potential spawning habitat by length. Surf smelt spawn has been documented at 59 sites in San Juan County. Pacific sand lance spawn activity has been documented at eight beaches. Four locations, Jackson’s Beach and Cattle Point on San Juan Island, and two Mackaye Harbor sites on Lopez Island, contain both surf smelt and Pacific sand lance spawning sites. From the 81 positive samples collected at 63 discrete spawning beaches on eight islands in San Juan County, a total of 12.7 linear miles is now documented forage fish spawning habitat.

Sand waves have been sampled intermittently from 2004-present. A combination of UW FHL class projects, mapping and benthic sampling, and a NWSI study in 2010-2011 found sand lance buried in the sand wave field off Turn Pt. in San Juan Channel. A few additional sand wave fields were sampled in 2010 and sand lance were present in those wave fields as well. A van Veen sediment grab was used and was very successful in capturing sand lance buried in sediment wave fields. The Northwest Straits have also posted a compilation of presence of sand lance in Puget Sound sampled with all types of gear (beach seine, tow net, van Veen grab (web site XXX).

Proposed Monitoring. The objective of previous forage fish spawning habitat assessment work in San Juan County was to identify sites utilized by surf smelt or Pacific sand lance for spawning. Because WDFW had completed some surveys prior to the San Juan County Forage Fish Project, the documented forage fish spawning habitat data set incorporates data from a 20 year time period. Little or no information is available on temporal changes in spawn density at individual sites, utilization of sites (seasonally and by year), consistency of spawning activity at known sites, or spawning activity at previously undocumented sites. The WDFW sampling protocol does support answering these questions if follow-up monitoring of forage fish spawning sites is conducted. Monitoring efforts should include periodic monitoring (every 5 years?) of documented sites, and exploratory surveys of potential spawn habitat as other spawning sites remain to be documented. This effort would also provide some insight into the question of how spawning habitat utilization may change over time.

Very little is known about the distribution of surf smelt and Pacific sand lance populations at other times of the year or during other life history stages. Monitoring efforts should be expanded to include assessment of larval and adult distribution and abundance. An acoustic survey that includes midwater trawling along a systematic grid of transects is the standard approach to monitor distributions of small pelagic fish species. Forage fish distribution monitoring would require development of sampling proceduresand should be conducted in consultation with WDFW (WDFW: Dan Pentila, LaConner office and Darcy Wildermuth, Mill Creek office). Additional expertise on acoustic surveying of pelagic fish species is available through the Fisheries Acoustics Laboratory at the University of Washington (UW contact John Horne). Some work is being done in southern British Columbia to determine genetic stocks of surf smelt; these efforts could provide a model for genetic stock monitoring efforts in the U.S. Potential Pacific sandlance habitat around the San Juan Islands is currently being surveyed and mapped by Gary Greene.

Another monitoring effort for age one sand lance could focus on the population when it is buried in sediment. An annual survey of the Turn Pt. sand wave field with a van Veen grab in winter months would capture their presence and abundance. The van Veen grab provides a standard unit of measure and has been documented to sample up to 70 fish in one grab. Population abundance and interannual variability could be obtained using this technique.

Existing Monitoring. Pacific herring. Washington Department of Fish and Wildlife conducts spawning site surveys in San Juan County annually, including Westcott Bay, Blind Bay, West Sound, Eastsound, Mud Bay, Hunter Bay, and Shoal Bay. Data are collected on herring spawn location, depth, timing, density, and submerged aquatic vegetation . WDFW’s herring survey record in the San Juans goes back about thirty years, but sampling has not been annual over that time period (Thompson et al. 2003). In 2004, Friends of the San Juans conducted exploratory surveys of additional, potential herring spawning sites throughout the County using the WDFW herring spawn deposition protocol. No new herring spawning locations were documented at that time. Forage fishes, when discovered in the proximity of sea lions and harbor seals (via acoustic surveys), are trawled and counted by WDFW (Darcy Wildermuth, personal communication). This work has been conducted annually since the 1980s.

Proposed Monitoring. Additional exploratory surveys of Pacific herring spawning sites could be conducted at these sites in the future as they were only sampled in 2004. Trends in submerged aquatic vegetation coverage at known herring spawning grounds can also be analyzed from existing data sets and included in future monitoring efforts using the same protocol. For example, discovery of dramatic eelgrass declines in Westcott Bay were first documented during the course of annual Pacific herring spawn surveys. Improved understanding of non spawning life history stages of herring and genetic stock identification monitoring efforts would also be informative to management of this key species (WDFW contact: Kurt Stick, LaConner) c. Pelagic Fish: Anadromous fish, Salmonids (MSA Target: Pacific Salmon) Salmon have declined from historic levels, but there are still harvestable populations of certain species. The decline was already noted over a century ago, but has continued through

62 harvesting, damming of spawning rivers, and habitat modification in watersheds, rivers and shorelines. The existence of genetically distinct stocks has been documented (WDFW 1993), with an assessment of their status, including extinction of some stocks. These data were compared to 2002 surveys (PSAT 2007, PSS 2011, Table 2-4), showing declines in healthy stocks of Chinook salmon and steelhead, and smaller declines in pink salmon abundance(?). Puget Sound chum and coho salmon abundances fared better during that time period, with an increase in the total number of stocks and number of healthy stocks, respectively. Sockeye stocks showed no change and the status of coastal cutthroat is currently unknown (both species occur in the MSA). Note: a large study of occurrence of juvenile Chinook salmon and forage fish in the San Juans was recently completed by Kurt Fresh, NOAA, and Eric Beamer of the Skagit System Cooperative. WDFW has listed Chinook salmon in Puget Sound, coastal bull trout, and Hood Canal summer- run chum salmon as “threatened “ since 1999. Puget Sound Steelhead were proposed as threatened in 2006 (PSAT 2007, Fig. 2-5, PSS 2011). Relatively recent assessments of west coast salmonids are provided by Busby et al. (1996, steelhead), Gustafson et al. (1997), Johnson et al. (1997, 1999, cutthroat), and Myers et al. (1998). Much of the MSA is critical habitat for juvenile salmon, which use eelgrass, kelp, marshes, and other shallow water habitat as foraging sites, as they do in other parts of the PSR (Schmidt et al. 1978abc, 1979ab, Simenstad et al. 1981b, Simenstad and Salo 1982, Wissmar 1988, Congleton and Smith 1996, Simenstad 2000, Toft et al. 2004, 2007, Toft and Starkhouse 2005). The ecosystem-level effects of reduced salmon populations may include poor survival rates for southern orcas, which are also burdened by substantial tissue concentrations of toxic chemicals, and heavy boat traffic. Orcas feed preferentially on Chinook salmon, now considered threatened in this region. The food resource for orcas may be reduced at present, compared to one or two centuries ago. The MSA Pacific salmon target identifies several indicators (Ind) for salmonids, including population density (e.g. CPUE in December) and size structure of all salmonid species (resident or returning stocks), abundance of juveniles by species, availability of brackish habitat (per PSAT method), and forage fish (adult, larvae, juvenile) abundance (as prey). Existing Monitoring. Pacific salmon target monitoring for the MSA Plan is based on the Monitoring tab from the Conservation Action Planning (CAP) Workbook developed during the 5 S Process for the MSA Plan (spreadsheet titled, Pacific Salmon MSA Monitoring.xls), where the Indicators and Key Ecological Attributes (KEA) for Pacific Salmon are highlighted. These Indicators and KEAs are included below with information regarding what current monitoring, assessments, or other information are available for each (see Appendix II).

Proposed Monitoring The WRIA2 Lead Entity for Salmon recovery is currently working with Salmon Recovery staff from the Puget Sound Partnership and the Puget Sound Recovery Implementation Technical Team (RITT) on the components of an adaptive management and monitoring plan. The steps to be undertaken in developing a local salmon recovery monitoring plan are noted below and as progress is made this section in the overall MSA Monitoring Plan will be updated. Current Status.  

63           

Development of Salmon Recovery Monitoring Plan: A monitoring plan is the basis of an adaptive management and monitoring approach. A salmon recovery monitoring plan is typically based on the limiting factors and VSP characteristics identified in each salmon recovery plan chapter. The first steps in creating this plan include: a. Create and review the template identifying the goals, hypotheses, strategies, and objectives of the local recovery plan chapter; b. Take these goals and convert them into monitoring questions or hypotheses. A clear monitoring question is generally directly linked to recovery goal measures, the scale of monitoring, and potential metrics or monitoring measurements. More than one monitoring question may be needed for each recovery goal; c. Identify what will be measured and what parameters or metrics will be used (e.g. riparian area, water temperature, etc.); d. Compare the list of what monitoring is needed with what information is currently being collected. Determine where there are gaps, areas in need of additional monitoring, or monitoring that does not need to occur; e. Determine whether additional resources are needed to conduct the monitoring

What are the different types of monitoring to be considered? There are several kinds of monitoring taking place across the Puget Sound to measure physical and biological attributes. Monitoring activities are generally categorized as follows: implementation, status and trends, and effectiveness/validation monitoring. • Implementation monitoring focuses on if projects were implemented and whether projects were implemented as designed (e.g. was the LWD project implemented and was the LWD placed in reaches as proposed in the project design?); • Status and trends monitoring focuses on gathering information on physical and biological indicators over a longer period of time. This information is used to assess changes over time in the physical and biological areas of interest (e.g. channel complexity, riparian density, and juvenile abundance);

64 • Effectiveness and Validation monitoring focuses on whether actions had the desired effect and whether the hypothesized relationships between the effect of the action and change in biota actually occurred (e.g. did the wood have the desired effect on the physical habitat and did the habitat changes induced by wood placement result in increases in fish or other biota?)

2.8. Marine Birds a. Overview - Marine and Coastal Birds (MSA Target: Seabirds) The MSA Seabirds target identifies population density of goldeneye (winter) harlequin ducks (winter), and rhinoceros auklets, and breeding colony size of glaucous winged gulls, pigeon guillemots and pelagic cormorants, as indicators and hatchlings/nesting pairs of pelagic cormorants and oystercatchers (Ind). It also identifies forage fish abundance as an additional indicator (Ind).

Existing Monitoring. Bird surveys have been conducted in the greater Puget Sound area including the San Juans since the late 1970’s. The Marine Ecosystem Analysis Puget Sound Project (MESA) was conducted in 1978 and 1979. The objective was to record the abundance and distribution of a wide range of marine species in the inland waters of northern Washington. Ten years later the Puget Sound Ambient Monitoring Program (PSAMP) contracted the Washington Department of Fish and Wildlife (WDFW) to develop marine bird surveys. In 1992 David Nysewander led a WDFW group in conducting aerial surveys of marine birds in Puget Sound and the Strait of Juan de Fuca. Their data is summarized at the web site of the PSAMP Marine Bird Density Atlas http://wdfw.wa.gov/mapping/psamp. In 2003 John Bower at Western Washington University (WWU) began redoing the MESA study using highly trained undergraduates. The three-year study was summarized at the 2005 Georgia Basin Puget Sound Research Conference (see PSAT 2007, PSS 2011, Table 2-6). The catalog of Washington Seabird Colonies (Speich and Wahl 1989) published by the U.S. Department of the Interior (USFWS, MMS) is another excellent resource detailing all nesting and colony locations mapped through the 1980s (many within the MSA). SeaDoc XXXX

The state of bird populations in the Puget Sound Region overall is discussed in detail in the 2007 PSAMP update (PSAT 2007, PSS 2011). Overall, there are more than 100 marine bird species in the Puget Sound Region, and approximately 30 percent of those are monitored by PSAMP and WDFW. Comparisons of bird populations in the late 1970s with those 20 or more years later, show significant decreases in many species including Brandt’s cormorants, grebes, surf scoters, pigeon guillemots, marbled murrelets, scaup (several), brant and long-tailed ducks, with only a few species showing a probable increase (harlequin ducks, common merganser) (PSAT 2002, PSAT 2007, PSS 2011). Scoters, dependent on eelgrass habitat and herring spawn, may be suffering from declines in herring populations (Bourne 1983, 1984, Lovvorn and Baldwin 1996, Lacroix 2002). COASST has volunteers walk beaches (at least 1km) and record all dead birds found by species; very few ever found (Kate Little, personal communication).

The WWU study, reported in the 2007 PSAMP update, (PSAT 2007, PSS 2011, Table 2-6) provides additional data showing strong declines (>20% since 1970s) in loons, common murres,

65 Bonaparte’s and Heermann’s gulls, ruddy ducks and both common and Barrows goldeneyes, plus increases (> 20%)in common loons, pelagic and double-crested cormorants, bald eagles, great blue herons, pigeon guillemots, rhinoceros auklets, white-winged scoters, northern pintails and American widgeons. This study estimates a decline of 27-47 percent for marine birds overall, and there is further information that declines have been most severe in and near urban areas along the eastern shores of central and southern Puget Sound (Casey Rice, pers. comm.). Nysewander et al. (2002) placed the decline in grebe and loon species at 64-95% over this same time period (see also Richardson 2000). See also Vermeer et al. (1994b).

Bald eagles were counted by WDFW on an annual basis beginning in the 1980s and continuing until 2002. Since then surveys have been sporadic with the most recent in 2005. These aerial surveys entail flying over historically known nests and then secondarily above other possible locations (Ruth Milner personal communication).

Proposed Monitoring. The San Juans were included in the MESA, PSAMP and Bower surveys. Any current marine bird monitoring program should build on the surveys of the past using protocols developed by MESA and WDFW for PSAMP. These surveys could be conducted every three to five years. Like the Bower surveys, these surveys could be conducted through highly trained volunteers such as Beach Watchers or members of the local Audubon chapter. On a finer scale, the San Juan County Marine Resources Committee (MRC) has recently released a Marine Stewardship Area Plan (MSAP) that pinpoints individual species as indicators of the health of the marine bird populations. These include black oystercatchers and pelagic cormorants. These two species should be monitored yearly and again this could be done with highly trained volunteers. Skagit and Island County Beach Watchers just completed at three year study of pigeon guillemots after receiving training from WDFW biologists. David Nysewander (WDFW) has been studying oystercatcher populations in the San Juans and has a protocol in place that could be used by local surveyors. WDFW could also provide guidance on surveying pelagic cormorants. At public hearings on the MSAP, participants wanted to know how they could become involved. Marine bird surveying is an excellent example of how citizen science can help provide data to understand the health of the ecosystem. When any citizen monitoring is done, we want to first get together with WDFW to make sure the correct protocols are used so we can compare across studies adequately. We certainly want to be sure that surveys done are in accordance with minimizing any harm to the birds themselves (i.e. not conducting surveys during sensitive seasons, etc). Also, another way citizens can get involved is by participating in the COASST beached bird survey work.

2.9 Marine Mammals (MSA Target) Marine mammals within the San Juan Archipelago include: southern resident orcas (killer whales); transient killer whales; minke, gray and humpback whales; harbor seals; Steller sea lions; California sea lions; harbor and Dall’s porpoises; river and sea otters (transient). The MSA Target identifies population size of harbor seals, harbor porpoises, and orcas as indicators (Ind), as well as breeding success of orcas. The MSA plan also identifies prey for orcas (salmon) and tissue concentrations of harbor seals as further indicators. Many other such indicators could be added.

66 The federal government, through NOAA Fisheries, is currently responsible for monitoring the status of all marine mammals listed above. In addition to its own activities, NOAA contracts with state and local partners to conduct the monitoring. NOAA also funds various research projects in San Juan County, and provides status reports on most of the above marine mammal populations on its website (www.nmfs.noaa.gov/pr/species/mammals/). In addition to the above marine mammal monitoring efforts, which are primarily focused on population trends, the San Juan County Marine Mammal Stranding Network (run by The Whale Museum), and the SeaDoc Society monitor marine mammal health, via NOAA Fisheries contracts. The Whale Museum’s Soundwatch Program monitors vessel activity trends around marine mammals (primarily killer whales) and vessel compliance with local guidelines and regulations, in order to help protect the marine mammals’ health and habitats. The Whale Museum also compiles all regional marine mammal sightings data (from public hotline, Soundwatch, whale watch operators, Orca Network and south sound sightings contractors) into data reports annually. a. River Otters and Sea Otters Once common along Washington’s coastline, sea otters (Enhydra lutris) were hunted for their pelts until the population went extinct. In 1969 and 1970 fifty-nine sea otters were reintroduced and a survey in July 2004 counted a total of 743 individuals (Jameson and Jeffries 2004). Compared to 1989 numbers, this total represents an annual average increase of 8.2%. The population appears to be growing, with individuals inhabiting regions from Kalaloch to the western Strait of Juan de Fuca. Unfortunately, the San Juan Archipelago currently does not have any known sea otter populations, although individuals have been observed off some of the islands. Potential effects of sea otters on subtidal benthic communities have been investigated experimentally in San Juan Channel (Carter and VanBlaricom 2002, Carter et al. 2007). Despite their name, river otters (Lontra canadensis) inhabit marine environments as well. Although not definitively demonstrated, river otters likely reduce sea urchin numbers thus reducing herbivory on kelp and increasing the quantity of this resource (J. Gaydos, pers. comm.). Currently the only monitoring of river otters is the necropsy work performed by Sea Doc as part of their ongoing collaboration with the San Juan County Marine Mammal Stranding Network (see above). b. Harbor Seals The harbor seal (Phoca vitulina) is a long-lived, non-migratory mammal, widely distributed across the northern hemisphere. Since they feed upon a large variety of species from fish to crustaceans, harbor seals bioaccumulate toxins and thus can serve as an indicator of marine contaminants. Likewise because they haul out on beaches and rocky shores for pupping, harbor seals are believed to be sensitive to anthropogenic disturbance (Angell and Balcomb 1982, Suryan and Harvey 1998). Currently NOAA and WDFW (Steve Jeffries) conduct routine censuses, in addition to studying prey and stress levels. The aerial surveys began in 1978 and were carried out every year through 2004 across the inland waters of Washington State and British Columbia (Jeffries et al. 2003). Since 2004 there have been no state wide counts; however surveys were conducted in 2006,

67 2007, and 2008 in San Juan County by Western Washington University and WDFW with NSF funding (Steve Jeffries, pers. comm. See http://www.biol.wwu.edu/mbel/?page=research ). This work has monitored abundance and distribution in addition to the dispersal of individual seals. Funding for further statewide counts is uncertain, but monitoring will continue as funds are available. Cascadia Research Collective regularly monitors pupping sites on Smith Island where they monitor natality, mortality and contamination trends (John Calambokidis, pers comm. 7/21/2009). The San Juan County Marine Mammal Stranding Network responds to all calls regarding stranded marine mammals, with harbor seals representing the vast majority of calls. A number of harbor seal carcasses are necropsied throughout the year, allowing the Stranding Network to gather baseline information on the health of the population as well as document any diseases or human-caused mortalities that may have occurred. Tissue samples are passed on to NOAA and other researchers for contaminant analysis. In addition, the Stranding Network has started the process of monitoring selected pupping sites using their trained volunteers. Once this program is established, it offers the opportunity of monitoring natality, mortality and survival rates on an annual basis in a cost effective manner. c. California Sea Lions Male California sea lions (Zalophus californianus) feed seasonally in the San Juan Archipelago. From fall until spring these opportunistic animals prey upon a wide variety of fish and invertebrates. Due to their large size (upwards of 400 kg) and abundant numbers, California sea lions can consume hefty quantities of salmonids, thus presenting a threat to salmon runs (Pat Gearin pers. comm.). Because there have been very few in the SJA, no work has been done specifically in this area. One thing to note is that the Stranding Network has been documenting the presence of female sea lions on occasion over the last couple of years. One of them was captured for rehabilitation in 2007 and was subsequently diagnosed with “domoic acid poisoning”, a condition that has been documented along the CA coastline since 1998. Since this population is now so large, it’s not unreasonable to expect to see more sea lions in our area, both male and female, as their feeding ranges expand. d. Steller Sea Lions Steller sea lions weigh up to 1000 kg and thus are the largest otariid in the San Juan Archipelago. Within the MSA, Steller sea lions use haul outs located at Whale Rock, Bird Rocks, Peapod Rocks, Speiden Island, and Sucia Island. WDFW has monitored the populations since the 1990s using aerial surveys and has found that Washington’s population have increased nearly 10% annually (Pat Gearin pers. comm.) (for haul out locations: http://wdfw.wa.gov/wlm/research/papers/seal_haulout/). There has also been considerable effort put into branding sea lion pups in southern Oregon and northern California. In follow up surveys, both in Washington and British Columbia, a number of these animals have been re- sighted which has helped monitor this stock and its dispersal (http://www.orcanetwork.org/marinemammals/sealionsightings.html). The Stranding Network has been getting reports of young males and possibly female sea lions appearing in our area over the last couple of years, suggesting range expansion for this population as well.

68 e. Porpoises Two species of porpoises inhabit the waters surrounding the San Juan Archipelago, harbor porpoises (Phocoena phocoena) and Dall’s porpoises (Phocoenoides dalli). Both species are small and feed on small non-commercially harvested fish, but their colorations are quite distinct. Dall’s porpoises have striking black and white marks and frequently follow boat wakes, causing many observers to believe they are juvenile orcas. Conversely harbor porpoises are nondescript and often avoid ships. Interestingly, within the San Juan Archipelago, Willis et al. (2004) documented that the two species hybridize, with male harbor porpoises mating with female Dall’s porpoises. Harbor porpoises were abundant in the 1940s but have since become a rare sight in the Puget Sound region (Puget Sound Update). Dall’s porpoises also used to follow the wake of boats in the San Juan Archipelago, but recently the numbers appear to have dramatically dropped (Brad Hanson pers. comm.). Since 1996 the National Marine Mammal Laboratory and Cascadia Research have performed semi-regular aerial surveys to estimate population sizes. The current goal is to survey once every five years, with the last survey conducted in 2003. However the next survey is not likely to occur until 2010 or 2011 (Jeff Laake, pers. comm.). The Stranding Network collects stranded porpoises on behalf of NOAA in San Juan County waters thus providing an estimate of disease and toxicity levels. The local abundance of harbor and Dall’s porpoise seems to have been in flux over the last couple of years with harbor porpoise numbers increasing and Dall’s numbers decreasing, although this is based on anecdotal observations by a number of whale watch operators and researchers. If the MRC is interested in monitoring harbor porpoise populations more closely (which might be a good idea since they seem to be in flux), data should be collected more often than the NMML/Cascadia surveys.

f. Orcas i. Southern Resident Killer Whales Populations of the Southern Resident Killer Whales have oscillated since the 1970s, showing almost no net population growth, while populations of the adjacent Northern Resident Killer Whales have increased substantially over the same time period (NOAA SRKW Recovery and Research Plan 2006). This population (SRKW) was listed as endangered in 2005 (NOAA), and has been the subject of studies to determine sources of mortality, including toxic burdens in their tissues.

Long-term monitoring plans are included in NOAA’s SRKW Recovery and Research Plan, through both the NW Regional Office and the Northwest Fisheries Science Center. Annual census and photo identifications have been conducted since 1974 and continue in conjunction with the Center for Whale Research. NOAA also collects fecal samples, prey samples, biopsy samples, and analyzes the samples for contaminants, stable isotopes, and stress levels. The Whale Museum and NOAA record acoustic data and study the effects of vessel traffic on orca behavior and vocalization. The Whale Museum annually compiles all killer whale sightings into an OrcaMaster data base, with maps and data available. No additional monitoring of these populations is recommended as part of the MSA monitoring plan.

69 g. Minke Whales The minke whales found in the MSA are considered part of the CA-OR-WA stock by the National Marine Fisheries Service, which is estimated to be at 806 (NMFS CA-OR-WA 2008 stock assessment. http://www.nmfs.noaa.gov/pr/pdfs/sars/po2008whmi-cow.pdf). This does not, however, include an estimate for the individuals that utilize the inland waters of Washington State and British Columbia. The best information on these inland whales comes from the Northeast Pacific Minke Whale Project (http://www.northeastpacificminke.org/) which started in the early 1980’s. This project photo identified 30 individual whales over an 11 year period. Minke whales in the MSA appear to show site fidelity and utilize different foraging techniques. The three foraging areas are the body of water between Waldron, Stuart and Speiden; the southern end of San Juan Channel; and the areas around Salmon, Hein and other Banks at the west end of the Straits of Juan de Fuca. Whales foraging around the banks tend to do so in association with birds feeding at the surface, while those at the other two locations tend to lunge feed. Both feeding activities are centered on herring and sand lance. The ongoing monitoring has detected a change in habitat usage over time. In the 1980’s all three sites were utilized for foraging, whereas the two northern feeding sites were abandoned during the 1990’s. Since 2005 whales have been found foraging in all three areas again. This was potentially attributed to changes in herring and sea bird abundance. The work of the Northeast Pacific Minke Whale Project is ongoing with an annual census, photo identifications, and investigations into feeding behavior by Jon Stern and colleagues. h. Humpback Whales Humpback whales occur in all oceans of the world, however they exhibit seasonal movements, spending winters in temperate and tropical waters, and summers generally in higher latitudes. They are endangered due to whaling through 1966. They feed largely on krill and schooling fish (NMFS 1991). Historically common around SJA, but whaling eradicated this population. Sightings of whales in Puget Sound now occur occasionally, and are becoming more common in the Strait of Juan de Fuca. SPLASH, the first complete census of humpbacks in North Pacific began in 2004 and continues to assess abundance, movement, population structure, and human impacts. Cascadia Research (John Calambokidis, et al.) are the repository for a photo identification catalog for this population and continue to ask for any photo ID shots from the public to continue monitoring this population. i. Gray Whales There are two populations of gray whales extant today; one in the western north Pacific which is critically endangered, and the other in the eastern north Pacific which has recovered to the point that it was de-listed in 1994. The eastern population of Gray whales migrate from Baja California (winter mating and calving ground) to the Bering Sea (summer feeding), but some seasonal residents stay in the Pacific NW during spring, summer, and fall. Gray whales do feed occasionally on midwater prey, but seem to specialize on benthic amphipods (Reeves et al. 2002).

70 Most years since 1967 the eastern Pacific population has been counted during its migration from Granite Canyon on the coast of California. The most recent stock assessment estimates 18,000 to 30,000 animals in this population (NOAA 2008 Gray Whale eastern stock assessment). The few Gray whales that become seasonal residents in the inland waters of Washington State mostly feed on ghost shrimp off Whidbey and Camano Islands. Cascadia Research (John Calambokidis, et al.) conduct annual census and photo identifications of these springtime residents, and many of the same individuals return year after year. Cascadia coordinates the central photo I.D. catalog for Gray whales in the Pacific Northwest and continues to ask for I.D. photos from whales in the inland waters. Gray whales are occasionally spotted in the MSA. j. Other mammals Other marine mammals in the MSA include elephant seals and Pacific white-sided dolphins. Several terrestrial mammals use marine resources, especially from the intertidal zone. These include raccoons and mink. According to the Stranding Network, elephant seal sightings are on the rise in the San Juan Islands. Over the last couple of years, they have documented two animals that have gone through complete molts (3-4 weeks time duration) on local beaches. There was also an elephant seal pup born on Race Rocks (first time documented) in March 2009. Just as with the other pinniped populations, the elephant seal population is large and it is possible that range expansion is occurring.

Section 3. Physical Environment and Habitat

3.1 Overview Puget Sound, a large and complex estuary, receives water input from the regional watersheds and from the ocean. Ocean water flows into Puget Sound at depth through the Strait of Juan de Fuca. However, the characteristics of this water flowing in from the Pacific Ocean are not constant. Water quality changes seasonally, interannually, according to large-scale atmosphere-ocean (e.g., El Nino-Southern Oscillation, Pacific Decadal Oscillation), and in patterns that we cannot predict, in response to other unidentified or random processes. The variation in oceanic seawater associated with these various natural processes has important implications for our ability to assess Puget Sound region water quality.

3.2 Marine Waters (Temperature, Salinity, Density, Stratification, Dissolved Oxygen) Ocean water coming into the MSA (Strait of Juan de Fuca) can fluctuate between high density waters with low oxygen and high nutrient content versus low density waters with high oxygen and low nutrient content, in response to upwelling/downwelling patterns generated by coastal winds and also from changes in coastal circulation. Of critical note is that high nutrient-low oxygen water can mimic conditions that exist during human-caused eutrophication. Therefore, estimates of water quality impairment may be misrepresented if ocean conditions are responsible, instead of human caused nutrient inputs and oxygen drawdown. Moreover, the Strait represents a “choke-point” on which to monitor in-flowing oceanic waters (deep layer) as well as the integration of out-flowing Puget Sound/Georgia Basin waters (upper layer), enabling valuable comparison of both water masses over time.

71 Current Monitoring. The Joint Effort to Monitor the Strait (JEMS) time-series of water quality stations in the Strait of Juan de Fuca was established in 1999 to fulfill a long-standing need for the water quality monitoring at the boundary to Puget Sound, as part of the Puget Sound Ambient Monitoring Program. The need for water quality data from the oceanic input to Puget Sound was a long-recognized one, but was logistically difficult to execute. The seaplane used by DOE to monitor marine waters could not be employed safely in the Strait due to swell. JEMS was established in 1999 as a response by DOE and PSAMP to this need. DOE used short-term funds (2-y) from King County Department of Natural Resources, the University of Washington’s Puget Sound Regional Synthesis Model (PRISM), and leveraged resources from Ecology, NOAA, and the UW Friday Harbor Laboratories (FHL) to establish a monthly monitoring program at three stations across the Strait of Juan de Fuca. The monthly cruise was conducted out of FHL facility, with technicians hired from FHL staff. The data were urgently needed by King County as boundary conditions for computer modeling of their proposed outfall.

JEMS data were cited at the recent Puget Sound-Georgia Basin Research Conference in numerous reports, including interpretation of nearshore vegetation (WDNR), macro-invertebrate dynamics (UW/WDFW), Hood Canal hypoxia (HCDOP), and general Puget Sound water quality (Ecology)). JEMS water quality data during the drought of 2000-2001 demonstrated a four-fold decrease in the exchange velocity through the Strait, with implications for a host of ecosystem effects, including pollution dispersion, larval transport, water quality, etc. (Newton et al. 2003). JEMS data were essential in documenting that the low oxygen signal in Hood Canal was not due to importation of coastal hypoxia (HCDOP 2005).

Figures 1-3 show the JEMS time-series of data for temperature (Fig 1), salinity (Fig 2), and oxygen (Fig 3) taken at the three stations that run N-S across the Strait of Juan de Fuca between San Juan Island and Pt. Angeles. Shown are contours of monthly data, beginning in Sept 1999 through Dec 2004. Aside from the seasonal cycle, one can see distinct inter-annual temperature (Fig 1) variation; this variation mirrors the ENSO-driven pattern (colder 2000, 2001, 2002, warmer 2003, 2004). Also, the higher salinity (Fig 2) signal from the 2000-2001 drought is clearly seen in the record. Seawater density, which is determined by temperature and salinity, controls the degree of stratification or layering of water in Puget Sound. There is also considerable inter-annual variation in the oxygen record (Fig 3).

Why is variability in these properties important to the MSA? Managers and researchers should be aware when changing ocean properties may be affecting the Puget Sound region:

• The variation in late summer dissolved oxygen concentration entering this region during this time-series is more than 1 mg/L (App. I, Fig. 3). This amount is five times the level for assessment of human impacts (0.2 mg/L) mandated for Washington State’s evaluation of water quality in response to the Federal Clean Water Act. • The variation in temperature and salinity alone is an important factor for species viability. • Variation in density structure determines many key ecosystem qualities: - when phytoplankton blooms occur; is food available when fish need it? -strength of basin flushing/circulation; how quickly does water exchange? - whether oxygen gradients are stronger or weaker; will natural conditions select for low oxygen or not?

3.3 Circulation (General Circulation Patterns, Upwelling) Current Modeling Efforts

The movement of water into and out of the San Juan Archipelago affects the biology and ecology of local species and communities of marine organisms. Currents within the MSA are important for transport of larvae, and movement of planktonic prey resources (Yao et al. 1985, Klinger et al. 2001, Klinger and Kido 2004). Much of the water that enters San Juan Channel comes from the Strait of Juan de Fuca, which also supplies the rest of the PSR (Holbrook 1980ab, Godin 1984, Lavelle et al. 1991, Mickett et al. 2004). On outgoing tides, water enters from the north, and this brings with it less saline water, and more suspended sediments, both originating from the Fraser River (Barrie and Currie 1997, 2000, Clague et al. 1983). a. Puget Sound Marine Environmental Modeling (PRISM) XXX b. Modeling Puget Sound Region Currents

5. Intertidal and Coastal Monitoring a. weather stations TBA XXXX

Section 4. Socio-cultural Targets

4.1 Overview Socio-cultural values were included as targets for protection in the Marine Stewardship Area Plan (MSA Plan 2007) in recognition that quality of life, cultural values, and the economy of the San Juan Islands are closely tied to a healthy marine ecosystem. Socio-cultural targets include:

• Enjoyment of the marine environment • Thriving marine-based livelihoods • Cultural traditions including aspects of ceremonial, subsistence, sustenance, and spiritual uses

4.2 Socio-cultural Targets. Table 4 provides a ranked list of stresses affecting the socio-cultural targets.

Table 4. Top stresses affecting the MSA socio-cultural targets. (MSA Plan 2007) Rank Stress Rating 1 Not enough fish to catch. very high 2 Not enough opportunity for commercial fishing very high 3 Fish contaminated with pollutants very high 4 Shellfish contaminated with pollutants high 5 Low availability of local seafood high 6 Not enough public access to beaches and shorelines high

73 7 Marine views and/or viewsheds impaired by buildings high 8* Not enough access to marine views and viewsheds high 9* Little knowledge of historical/current marine cultural sites & traditions high 10* Too few cultural activities and traditions are practiced high 11* Not enough fish landed for local markets high 12* Too few local vessels involved in commercial fisheries high 13* Not enough local fishermen involved in the commercial fisheries high 14* Wages too low in marine-based livelihoods high 15 Not enough opportunity for sustenance fishing high 16 Reduced quality of marine recreational experiences high 17* Not enough big fish caught high 18 Marine cultural sites and practices aren't respected high 19 Not enough opportunity for recreational fishing high 20 Not enough shellfish available to catch high 21 Not enough access to shellfishing areas med 22 Inadequate marine transportation infrastructure med 23 Not enough boating facilities for residents' use med 24 Not enough wildlife to view med 25 Locally caught/raised seafood is too expensive med 26 Not enough opportunities to learn about the marine environment med 27 Little diversity in marine-based livelihoods med 28 Not enough opportunities for marine research low 29 Not enough boating facilities for visitors' use low 30 Shellfish are too small low 31 Not enough diversity of marine recreational experiences low * - equal value/tied with the stress above.

Proposed monitoring. Baseline definitions and assessment need to be established xxxx. Monitoring to measure progress in achieving the socio-cultural benchmarks should be conducted at five-year intervals.

Benchmark SC-1: Year-round recreational, commercial and sustenance fishing opportunities exist for county residents, tribes with usual and accustomed fishing rights and visitors by 2037. Monitoring method: survey people engaged in recreational, commercial, and sustenance fishing.

Benchmark SC-4: By 2017, locally harvested marine species pose insignificant risks to human health. Monitoring method: Inventory recreational and commercial shellfish harvest sites that are open, conditionally open, and closed. Document incidences of shellfish harvest and fishing advisories.

Benchmark SC-5: The majority (greater than 50%) of San Juan County residents and frequent visitors to the San Juan Islands are aware, involved, and feel ownership of the MSA. Monitoring method: Survey public knowledge of the MSA and stewardship behaviors. Assess citizen participation at events, environmental training, and volunteer opportunities (Beach Watchers, Marine Naturalists, citizen monitoring). Document number and sustainable activities of businesses, government, and schools that engage in sustainable practices and offer green goods and services.

Benchmark SC-6: The scenic and natural marine environment is available for human enjoyment. Monitoring method: Conduct a survey to assess availability, adequacy and use of recreational sites, facilities, and public access to the marine environment. Assess adequacy of outreach programs that foster sustainable use of these opportunities.

Section 5. Monitoring Threats to the MSA

5.1 Climate Change (Threat No. 2, High) a. Changes in Temperature and Precipitation Global air temperature has increased substantially over the past century, mostly as a result of the huge quantities of carbon dioxide added to the atmosphere by human use of fossil fuels. Air temperature in this region (Puget Sound Region) has increased at about twice the worldwide average (Ref. xxx) Even if there are worldwide measures put in place to curb carbon emissions, global warming is predicted to continue for many decades before ceasing or reversing, and thus the changes we have already seen in the oceans are only the beginning of many more to come. The direct effects of increased air temperature will mostly impact the intertidal region. However, rising air temperatures are linked to accompanying changes in cloud cover, wind patterns, precipitation and snowpack. These associated climatic factors exert effects on most of the ecosystems of interest within the MSA. In many cases, it is not average temperatures, but temperature extremes that exert the largest effect on intertidal communities. For instance, extremely hot days that correspond with mid-day low tides are associated with mortality events of intertidal organisms (Helmuth et al 2006). Thus, effects of rising air temperatures can manifest themselves as sudden, episodic community shifts. b. Sea Surface Temperature (SST), Ocean acidification (OA) Sea surface temperature in the Puget Sound region has also increased substantially over the past century. The best long-term record comes from Race Rocks, in the Strait of Juan de Fuca off Victoria, B.C., which goes back to the 1920s (Figure 4). This data set (http://www.racerocks.com/racerock/data/seatemp/seatemppast.htm) shows an increase of around one degree Centigrade, most of which occurred since the 1950s. In addition to a general warming trend, there has also been a shift to higher temperatures (1977 to 1999) due to the Pacific Decadal Oscillation (Miller et al 1994, http://www.intellicast.com/Community/Content.aspx?ref=rss&a=151). One degree is more than enough to affect the growth, distribution, breeding and larval success of marine invertebrates and fish (Barry et al 1995, Helmuth 1999, Helmuth et al. 2002). Pacific cod and walleye pollock, for example, are near their southern limit in the Puget Sound region, and higher water temperatures may already be suppressing their spawning success (PSAT 2007, PSS 2011); the same may be

75 true for the Pinto Abalone. This rapid increase in temperature is projected to continue through the next century and beyond, so we can expect concomitant large changes in the abundance and north-south distribution of many of our locally common species. Higher temperatures are likely to have direct effects on physiology, behavior, growth and distribution of intertidal species (Bertness and Schneider 1976, Gutermuth and Armstrong 1989, Wootton et al. 1996, Harley and Helmuth 2003, Hoffman et al. 2003).

The change in ocean temperature, and the increased amount of carbon dioxide coming into the ocean from the atmosphere, have already produced a measurable change in ocean acidity, resulting in surface waters that are now more acid than they have been for many thousands of years (Feely et al. 2004, Sabine 2004, Orr et al. 2005, Caldeira and Wickett 2005, Wootton et al. 2008). As acidification increases, the depth at which calcium carbonate dissolves (rather than precipitates and crystallizes out of solution) becomes more shallow and thus affects more of the upper water column where most organisms live. This effect is predicted to be larger than average in the Northeastern Pacific Ocean, and thus in the water entering the Puget Sound Region.

Increased acidity makes it harder for creatures that deposit calcium carbonate shells to calcify, including corals, mollusks, barnacles, and coralline algae as examples. Planktonic organisms, including larvae of marine invertebrates, often use external shells for protection, and those shells do not develop properly as acidity increases (pH decreases) (e.g. pteropod mollusks, Fabry 1990). Additionally, recent evidence suggests that organisms grown under acidified conditions may be more susceptible to other environmental stressors such as increased temperature (O’Donnell et al 2009). Photosynthetic plankton, including calcifiers such as Coccolithophores, exhibit a more complex response to ocean acidification as the detrimental effects to calcification conflict with the positive effects to photosynthesis (e.g., Iglesias-Rodriguez et al. 2008). The overall effect of acidification will be similar to that of temperature increase, favoring some species and groups and reducing others. Secondary effects, such as producing conditions that favor predators over prey, complicate predictions further (e.g., Gooding et al, 2009). One difference between acidification and temperature effects is that species cannot shift north or south to escape the change because it will be so widespread. Both changes will have serious consequences for the species that occupy this region, and we cannot predict accurately which species will be able to adapt, shift distribution, or which may disappear altogether. Another complication is that it will be hard to determine if species are responding to these large-scale changes, to present or past harvest effects, toxic contamination, or some combination of these factors. The effects are also not likely to be additive; for example increased temperature could reduce the chances for recovery from past harvesting in the pinto abalone (a cold-adapted species), and increased acidity could make their larvae less able to survive and provide new recruits for the population.

Existing Monitoring. Sea surface temperature is monitored at DOE buoys and at NOAA tide stations. UW FHL also monitors both air and sea surface temperature at Cantilever Pt., just north of Friday Harbor (http://faculty.washington.edu/ecarring/weather.html), and water temperature at five depths, plus

76 salinity and irradiance at one depth. The longest constant SST record is from Race Rocks, south of Victoria and Southwest of the MSA (Figure 4). Environmental temperature data should be incorporated into a GIS database for intertidal and subtidal survey locations. In many cases, extreme temperatures are likely to have a greater effect on communities than average temperatures. Real-time temperature data showing extreme temperature events should trigger rapid re-assessment of high intertidal survey sites to document potential community shifts, for example. The various chemical components involved with ocean acidification require laborious analysis and little data exist for the region. FHL is in the process of developing suitable analysis capability, and will begin regular data collection for carbonate chemistry in the near future (2011).

5.2 Potential Sea Level Rise (Threat No. 0, Medium) Sea level rise is predicted to be over half a meter in the MSA over the next century, and close to a meter in lower Puget Sound (PSAT 2005). However, recent melting in polar regions has been greater than predicted, and it is quite possible that these predictions of sea level rise are on the low end. The expected result of sea level rise is a change in coastal habitats, with the creation of new wetlands, and new connections between existing wetlands and marine waters (Mofjeld 1992). Many marine and brackish water creatures will be able to migrate or have successful larval settlement in the new areas, but some previously brackish areas may become fully marine with a concurrent replacement of species. Foraging areas for juvenile salmon are likely to change as this occurs along with habitat loss for shorebirds (Galbraith et al. 2002). Buildings, docks, and shoreline structures may have to be abandoned or rebuilt inland as this rise occurs. There may also be pressure from landowners to add shoreline armoring to prevent erosion on some shorelines; such engineering will require careful evaluation for unintended consequences to adjacent biota.

Existing Monitoring. NOAA tide gauges throughout the PSR, including one at UW FHL, give precise tidal heights and average sea level. Proposed intertidal and shallow subtidal monitoring programs should incorporate descriptions of vertical survey positions so potential community shifts due to sea- level rise can be properly attributed. Intertidal surveys should incorporate design elements (e.g., cross-shore transects, large-scale referenced photographs) that permit identification of vertical distribution shifts. Shallow subtidal surveys should seek to identify communities at risk from the potential habitat changes.

5.3 Toxic Contaminants (Threat No. 6, Medium)

a. Overview

77 Aquatic organisms are sensitive to a number of metal ions, such as copper, zinc, and arsenic, which may be naturally occurring or anthropogenic; as well as a wide range of organic compounds introduced into the environment by human activity including lawn and garden chemicals, household cleaners, paints and solvents, and lubricants, coolants and brake dust from motor vehicle use. In addition, human residential and agricultural waste is rich in nitrates, which can boost algal blooms in aquatic ecosystems, including the toxic algae that can poison fish and make shellfish unsafe for human consumption (e.g. mercury, Zisette et al. 2002). Table 2 lists the chemicals of highest concern as classified by the Puget Sound Action Team, with added comments.

78 Table 5. Chemicals of highest concern in Puget Sound (source: 2007 Puget Sound Update, PSAT 2007, PSS 2011). Chemical Source Regulatory status Toxic category Metals Tributyl tin Anti-fouling paint on boats Banned Endocrine (organometallic) worldwide disruptor Lead Car batteries, gasoline, old Removed from Neurotoxin paint gasoline, paint. Mercury mostly generated by the Heavy metal burning of coal and wood, poison but also released into the environment by production and disposal of batteries and fluorescent light bulbs, and by the decomposition of woody material in some artificial lakes and ponds Arsenic Lead arsenate pesticide used Pesticide banned? Poison in local fruit orchards; EPA pushing for geological sources lower drinking water limits. Cadmium Geological sources Extremely toxic and bioaccumulative Copper Boat anti-foulant; lumber Permitted Algicide, preservative bacteriocide

Organic compounds Polychlorinated Widely used as Banned in the Endocrine biphenyls (PCBs) insulating fluid in 1970s disruptors electrical transformers. Polycyclic aromatic produced by burning coal, Carcinogens hydrocarbons (PAHs) petroleum or wood; in petro- based road tars and creosote. Pesticides Home, garden and farm use; All banned for Neurotoxins; Organochlorine use in the United DDT was an agricultural pesticides States endocrine aldrin, dieldrin, DDT, disruptor in and toxaphene and the raptors

79 organochlorine fungicide hexachlorobenzene Dioxins and furans generated by the Carcinogens production of paper and wood pulp products and burning of paper, particleboard and coal Polybrominated widely used as flame- Most congeners Endocrine diphenyl ethers retardants but now being banned; disruptors; (PBDEs) gradually phased out of decaPBDE in structurally production and use; phase-out. similar to thyroid hormones Phthalate esters Plasticizers in linoleum, fan Phased-out in Endocrine belts, PVC pipes, IV tubing; medical plastics disruptors solvents in cosmetics. and some cosmetics Bisphenol A (BPA) Component of Banned in plastic Endocrine polycarbonates toys in some disruptor cities. Nonyl phenol Commercial detergents; Endocrine surfactants disruptor 17b-estradiol, Natural and synthetic human Endocrine ethynylestradiol) hormones disruptor

Persistent Bioaccumulative Toxins (PBTs). This group of contaminants is generally not being monitored regularly within the MSA. Information on monitoring programs throughout the Puget Sound Region can be found in the PSAMP 2007 Update (PSAT 2007, PSS 2011). Persistent Bioaccumulative Toxins (PBTs) in the food web include those chemicals that do not degrade rapidly and often accumulate in fatty tissues of animals, especially those higher in the food chain (herring, salmon, birds, marine mammals). WDOE identified PCBs, PBDEs, aldrin/dieldrin, benzo(a)pyrene, chlordane, DDT, dioxins and furans, hexachlorobenzene, mercury and toxaphene as those PBTs of greatest concern (PSAMP 2007). Endocrine disrupting compounds (PSAMP 2007, Table 4-6) and surfactants are also of becoming of increasing concern. Urban marine sediments are large repositories of PBTs (Long et al. 2005), but sediments in most other parts of the Puget Sound Region are relatively uncontaminated. Mayer and Elkins (1990) examined agricultural pesticide runoff into Padilla Bay just east of the MSA. Polycyclic aromatic hydrocarbons (PAHs) are another group of toxic and carcinogenic compounds that result from burning fossil fuels and other organic matter including wood (PSAMP 2007, Table 4-4). Most PAHs in the marine environment come from rivers, streams and stormwater runoff as well as from the atmosphere, from exhaust emissions. PAHs are common in sediments, and in areas with creosote debris, and in organisms that frequent those habitats.

80 Urban sediments in the Puget Sound Region contain concentrations of PAHs that are known to cause liver disease in fish (PSAMP 2007, Fig. 4-27 to 4-32). PAHs in mussel tissue in central Puget Sound were 10-20 times those at non-urban sites (e.g. Cape Flattery, PSAMP 2007 Fig. 4- 26, WDOE data) although none of the sites studied were within the MSA (nearest sites were Strait of Georgia, Bellingham Bay). There is a general trend of decreasing PAHs in mussel tissue since the 1980s, and decreased risk of liver lesions in English sole in highly contaminated sites (creosote facility) after sediments were capped (PSAMP 2007, Fig. 4-32 to 4-34). Removal of creosote treated wood, debris, and gradual replacement of existing pilings is a goal of the PSP because these materials can release creosote into the marine environment even when 60 years or more of age (Dinnel 2005, in Broadhurst 2005). Whatcom and Skagit counties began a creosote removal program which removed 275 tons of debris from 112 miles of shoreline during 2002-2005 (PSAMP 2007). Control of stormwater runoff from impervious surfaces is another important way to reduce PAHs entering the marine environment.

Key vectors of anthropogenic toxics in the San Juan Islands include residential and commercial wastewater discharge and septic leakage, the direct outdoor application of toxic products, and surface water runoff from roofs, roads, and fields. Some toxics are water soluble, dissolving and moving relatively quickly horizontally from land to sea, or downward into aquifers. Most are hydrophobic, however. They adhere to silt particles, and are transported as suspended solids to be deposited eventually in freshwater or marine sediments, where they can persist for months to years. Some are stable indefinitely.

While dissolved toxics are taken up through the membranes of aquatic organisms, including the gills of fish, toxics adsorbed to sediment particles enter the food chain through detritivores, such as marine worms, and may bioaccumulate in the tissues of successive consumers. Toxic sediments may also be resuspended by aquatic animals’ burrowing and foraging activities (bioturbation), or by human activity such as prop wash, dredging, or the removal of over-water structures.

It is not yet known what proportion of the toxics in our local marine environment is attributable to San Juan County residents and businesses, and what proportion is swept in through the islands’ waters by tides and currents from other parts of the Puget Sound Region—in particular from major cities such as Vancouver, Victoria, and Seattle, which likely provide the greatest input to our waters. There is evidence that nutrients, and perhaps certain contaminants, are carried into the islands’ waters from the ocean more than 100 km distant. Atmospheric deposition has recently been identified as the most likely source of some toxic metals and organic compounds, such as PCBs, in the Fraser River, as well as Mountain Lake (Orcas Island). Thus while San Juan County’s residents and businesses can play a role in reducing contaminants in freshwater as well as marine ecosystems in the islands, protecting and restoring our marine environment must also involve the cooperation of neighboring U.S. and Canadian communities. b. Specific local threats

At the State level, particular attention has focused on a small number of especially persistent and bio-accumulative toxics (PBTs), most of which are already banned in the United States, and therefore are chiefly “legacy contaminants” still found in industrial sites, solid waste dumps, and sediments: see PCBs, PBDEs, Organochlorine pesicides, PAHs, Dioxins, and mercury (Table 5).

81 State sponsored assessments of PBTs have focused on urban areas where sediments have proven to be significantly contaminated (Long et al. 2005). Comparatively little is known about sediments in the San Juan Islands. It seems likely that products of fossil-fuel consumption and smokestack industry throughout the Puget Sound Region have reached the islands via airborne and waterborne deposition, in unknown concentrations. Relatively few priority PBTs appear to be generated within the islands, however. PCB-filled transformers were long used by the local power utility, OPALCO, while creosote and other wood preservatives traditionally used in over-water structures can contain dioxins, furans and PAHs, as can the road-paving tars that are still widely used here by the county government, as well as private landowners (Barsh et al. 2007).

A single recent State study (Seiders et al. 2007) found measurable PCBs, PBDEs, organochlorine pesticides, and mercury in a small sample of rainbow trout in Mountain Lake (Moran State Park). Rainbow trout are planted annually in the park, however, and the length of time the sampled fish had been resident in Mountain Lake was unknown. Nonetheless, the data suggest that atmospheric deposition is significant, since the basin occupied by Mountain Lake is undeveloped except for foot trails and a dirt road. Young et al. (1993) also found PAHs and PCBs in mussels from the Puget Sound Region.

During high rains untreated sewage overflow from Victoria, Vancouver Island, continues (?) to be a threat to the San Juan Islands. There are two urban wastewater treatment plant outfalls, one only 11 miles from the west side San Juan Island. Routine monitoring of WWTP effluents rarely consists of more than the standard water quality parameters. For organic contaminants that escape the treatment process, more sophisticated methods are required. Ultraviolet absorbance of seawater is a quick and convenient indicator of dissolved organic matter (DOM) in relatively undiluted sewage outfalls. UV absorbance measurements at the Macaulay Point and Clover Point outfalls correlated well with standard water quality parameters for effluent levels in these areas, indicating an acceptable dilution of 500:1 within the vicinity of the outfall diffusers (Balch, et.al., 1975).

At the same time, the specific industrial and agricultural history, as well as contemporary demography of San Juan County, suggests a number of local toxic issues not prioritized by the State. While organochlorine pesticides were heavily used in some parts of this State to control rootworms and protect stored seeds, San Juan County agriculture was long dominated by fruit orchards, which routinely used lead arsenate to control pests. A preliminary survey of San Juan County streams found quantifiable arsenic in several watersheds, but was unable to make a connection with agriculture, and inferred that the source is geological (Barsh et al. 2008).

Cadmium, an extremely toxic and bio-accumulative metal, has been found in elevated concentrations in shellfish in many parts of the Puget Sound Region, including the islands, and in some San Juan County sediments (Kruzynski 2004, Takesue et al. 2006). Once again, the source may be geological but this remains to be investigated adequately. Motor vehicle brake pads are a source of cadmium, and road dust could be a vector to aquatic ecosystems.

San Juan County has an exceptionally high proportion of shoreline and, as a result, a large per capita number of boats. Anti-fouling treatments such as copper and zinc are not on the State priority list, but should be assessed here in the islands, especially in low circulation bays where many marinas and private docks are concentrated.

82 Above all, San Juan County today is residential, with a rapidly growing population along the shoreline. Most household-use pesticides, herbicides, and cleaners are highly toxic to aquatic organisms, and many of them can persist long enough in soil and water to make the short journey from island lawns, gardens, and homes to marine waters. An ongoing assessment supported by the Washington Department of Ecology has already found pesticide residues and surfactants in San Juan County lakes, ponds and streams (R. Barsh pers. comm.). We can do much more to manage this class of toxics because informed local residents can choose to use less, or to use the least toxic products from among those available.

There is also concern about the routine disposal of pharmaceuticals, as well as pharmaceutical residues and breakdown products in waste water and septic seepage. A growing number of such compounds have been shown to have physiological effects on aquatic organisms, such as altering sexual development or reproduction (endocrine disrupters). Their concentrations in San Juan County waters are not yet known. c. Baseline data and existing monitoring Baseline assessment and monitoring of contaminants in water and sediments has at least three important applications: (1) evaluating how well we are doing at reducing the islands’ toxic inputs to marine environments; (2) determining the extent to which marine water quality in the islands depends upon the management of urban waste from outside San Juan County, for which State, municipal, and international cooperation is required; and (3) providing a basis for evaluating the impacts of any future tanker spill or similar disaster. It is also an opportunity to engage citizens in useful research and to foster a core group of more informed consumers and businesses. See also: (Waldichuk, 1983, EPA 1991, Newton et al. 2002, Ruef et al. 2004).

A major challenge for chemical monitoring is the expense of reliably identifying and measuring specific compounds. Thousands of toxic compounds are used around the Puget Sound Region, and everyday products such as shampoo, hand soaps, and garden sprays can contain a bewildering variety of related toxic chemical species. More than 20 different chemical species of pyrethroids alone are found in pesticides currently sold in San Juan County, for instance. Since it is not technically feasible to measure individually all local chemical inputs to the marine environment, much less the inputs from Puget Sound Region cities, a panel of representative toxic compounds should be selected on the basis of current and anticipated conditions. Phenanthrene can be used as an indicator for total PAHs, for example, or linear alkyl sulfonates (LAS) for all surfactants, if creosote and soaps have been identified as monitoring targets. Initially, more research is needed to identify the contaminants that currently threaten aquatic ecosystems in San Juan County, either because they are already present at or near the level of biological effects, or because they represent specific threats from anticipated future growth in population, boating, and shipping.

A related issue is the desired level of precision in measuring these contaminants. Federal and State agencies have mainly been concerned whether particular compounds exceed legal standards for maximum concentrations in water—generally drinking water. As our knowledge of the physiology of particular toxics increases and the sensitivity of our instruments improves, legally permitted maximum concentrations are typically lowered in newer regulations. For monitoring purposes, it is important to make precise measurements so that trends can be detected as early as possible, even if concentrations are well below current legislated safety

83 thresholds. For example, maximum allowable arsenic in drinking water is currently 10 ppb (g/L), but the EPA has been advocating an upper limit of 5 ppb and a goal of no measurable arsenic (currently approximately < 0.1 ppb).

Sampling design is also an important consideration. For early warning, it may be best to focus on “hot spots”, such as low-circulation bodies of water, where toxic inputs are most likely to accumulate fastest and attain measurable concentrations soonest. At the same time, a monitoring design should include relatively uncontaminated, high-circulation sites that represent the best available water quality conditions as standards for comparison. Additional sites may be included because of their ecological significance (e.g. salmon and herring nurseries) in providing observation of direct links between water quality and wildlife.

Bulk toxicity assays can also play a useful role in early warning design. Toxicity is the measurable effect of water samples, including all dissolved solids, on a standard test organism such as Vibrio fischeri or Daphnia magna. If the sample has a consistent adverse effect on the test organism across a range of dilutions, it is clear that some toxic substance, or substances, is present, even if the sample does not contain the specific toxic compounds that are already being monitored. Such a result warrants an investigation to identify the “new” chemical threat and its source.

Friday Harbor Laboratories’ K-12 Science Outreach Program (FHLSOP) has been collecting data on dissolved oxygen, pH, turbidity, and fecal coliform bacteria in selected San Juan County streams since 2002. Most of these streams have been included in the baseline studies of toxic metals, pesticides, herbicides, and surfactants conducted by Barsh and his colleagues at Kwiáht in 2007-2008. In collaboration with the San Juan Nature Institute, Kwiáht has begun training local volunteers on four islands to conduct routine freshwater quality monitoring that includes nitrates, phenols (petroleum derivatives), surfactants, and some metals. San Juan County Planning & Community Development and Kwiáht have begun collecting baseline toxicity data from many of the same watersheds, with a view to long-term systematic toxicity monitoring by county staff. Contaminants in marine waters and sediments, as well as bio- indicator species, need to be included in these emerging efforts as the basis for a systematic multi-party monitoring plan with permanent sampling sites and a carefully constructed list of chemical targets that reflects actual conditions in San Juan County. FHL also collected detailed data on chemical contaminants in Beaverton Creek during 2007 (analysis by XXX labs).

The University of Washington Friday Harbor Labs recently acquired tools for trace chemical analysis including a Liquid- Chromatography Mass Spectrometer (LC-MS) equipped with Electrospray Ionization (ESI) as well as a Gas-Chromatography Mass Spectrometer (GC-MS). These can be used for precise and accurate measurements of endocrine disruptors like Bisphenol A and surfactants. Adding a "softer" ionization source to the LC-MS could allow for measurements of other PBTs like PCBs and PBDEs. Initial LCMS tests with the surfactant 4-n- Nonylphenol showed a limit of detection in water samples of 10 ppb after solid phase extraction, which is below the Lowest Observed Adverse Effect Concentration (LOAEC) reported by Gray and Metcalfe (1997) causing developmental effects in Rainbow Trout.

84 Funding is a significant constraint to be addressed. County staff, citizen scientists, and local students can be trained and supervised by organizations already engaged in the study of contaminants in San Juan County waters, but the cost of analytical instruments and laboratory supplies is not trivial. High technical standards must be maintained for public and political credibility, as well as the creation of useful baseline data sets. Of immediate concern are local “emerging contaminants” defined as chemicals associated with urban development and population growth, chemicals recently identified as contaminants, and chemicals that are airborne and waterborne from non-local sources. Table 3 is a suggested list of emerging contaminants for prioritizing future monitoring.

Table 6. Emerging contaminants of local concern Chemical Reason for concern Regulatory status Toxic effects Deca PBDE Lingering flame retardant Phaseout of Deca in Thyroid disruption and to be phased out by 2013; Washington starting immuno-suppression in up to 70% by weight in in 2011; worldwide whales; highly fabrics and plastics. ban of the lower bioaccumulative and brominated persistent congeners Phthalate Increased residential and Phase-out under Possible endocrine plasticizer di(2- commercial development consideration; disruptor in humans ethylhexyl) industries switching phthalate to new plasticizers (DEHP) Nonyl phenol More toxic breakdown EPA/industry Endocrine disruptor, product of alkylphenol agreement to halt use but not as persistent as polyethoxylates (nonionic in liquid detergents in others. surfactants) 2013 and powders in 2014. Triclosan Increased use of personal Under review Endocrine disruptor care products Bisphenol A Toxic breakdown product Ban considered; Endocrine disruptor of polycarbonate plastics industries switching and epoxy glues to new plastics. Polyfluoro In non-stick cookware On EPA’s Potential octanoic acid fluoropolymers and Contaminant developmental and (PFOA) waterproof clothing; low Candidate List cancer effects blood levels in humans Ethinylestradiol Synthetic human hormone Advocacy for lower Most potent estrogenic (one of that will increases with dose timed-release agent in marine numerous

85 pharmaceuticals population. birth control patches. vertebrates of concern) Pyrethroids Leading insecticide; heavy Permitted; less toxic Potent insect and use against carpenter ants. bifenthrin invertebrate neurotoxin; replacement now available. Mecoprop Substantial levels found Permitted and Analog of plant growth (herbicide) recently on San Juan Island available in local auxins; unknown stores. effects on benthic organisms.

High levels of the PBDE flame retardants in fabrics, upholstery, construction plastics and electronics continues to threaten our salmon and whale populations. The lower brominated PBDE congeners are banned worldwide and now in the US. However, the toxic and most bioaccumulative decabromo congener (deca BDE) is in a slow phase-out in the US and still a concern in the Salish Sea. The ubiquitous plasticizer DEHP, a suspected endocrine disruptor and a major contaminant in Tacoma and Seattle, is found in low parts-per-billion (ppb) levels in a preliminary study of several local water samples (Bell et al. 2010). These levels, while lower than those in King County, bear watching as Island populations grow. Nonyl phenol is an environmental breakdown product of the polyethoxylate class of nonionic detergents and a wide-spread Salish Sea contaminant. Nonyl phenol, in trace amounts, was identified in local samples by liquid chromatography-mass spectrometry ( S. Iverson, pers. Comm.). The biocide triclosan has a chemical structure resembling that of the thyroid hormones. Triclosan is less bioaccumulative than the PBDEs, but listed as an endocrine disruptor. The biocide is in cosmetics, dish detergents, toothpaste, and industrial germicides. Environmental bacterial resistance is occurring (Madrona Murphy, pers. Comm.). Low? Levels of triclosan were recently found in San Juan County in an immunoassay screen (with middle school students, at Friday Harbor Labs), conducted by KWIAHT (Russel Barsh, pers comm.). Bisphenol A, another endocrine disruptor resembling estrogen and thyroid structures, constitutes 70% of the polymeric structure of polycarbonate and epoxy plastics. Consequently, bisphenol A is continually released during environmental degradation of these plastics, and will continue to be of concern until manufacturers introduce replacements. Polyfluoro octanoic acid (PFOA) is on EPA’s list of unregulated drinking water contaminants (EPA, 2009). “Most Americans have about 5 ppb of PFOA in their blood…and potential health concerns include developmental toxicity, cancer, and bioaccumulation” (Richardson 2008). The most potent estrogenic disruptor is the synthetic female hormone, ethynyl estradiol (EE). It is over one hundred times the potency of estradiol and over a million times the potency of nonylphenol, bisphenol A and DEHP (King County 2007). EE was not detected in marine waters, “below all but six literature-based effect concentrations” in lakes, but in streams/rivers “two to four times higher than in lakes and within the range documented in laboratory studies to

86 cause adverse effects in several fish species.” (King County 2007). This study suggests that EE levels may be of concern in local streams and stormwater runoff near residential developments if not in sewage plant effluents. It is important to note that an adverse effect on fish in a laboratory setting does not necessarily extrapolate to their natural habitat (Mills and Chichester 2005). Pyrethroid insecticides are toxic to trout and aquatic invertebrates. Levels of concern are detected in selected, local sites, but adverse effects are yet to be documented (Barsh et al. 2010). A new, less toxic replacement for bifenthrin is being brought into use by a local abatement company (Barbara Rosenkotter, pers. comm.) Mecoprop, a newer congener of the chlorophenoxy herbicide 2,4-D, was found at up to 8 parts- per-million (ppm) in several soil sites on San Juan Island, in contrast to low or nondetectable levels of an extensive panel of metals, pesticides, phthalates and fuels (Damron et al. 2010). Although mecoprop is considered to have relatively low toxicity, the EPA is requiring endocrine screening when these tests become available (EPA 2007). Mecoprop degrades in soils to a methylchloro phenol, whose predicted no effect concentration for aquatic organisms is 50 parts- per-billion (ppb) (Niemela and Tyle 1989).

Table 7. Anticipated emerging contaminants of local concern Chemical Reason for concern Regulatory status Possible toxic effects Alkaline copper Wood preservative Replaced banned Copper oxide fungicide quaternary (ACQ) for decay-resistant chromated copper and a quaternary deck and foundation arsenate in 2003 ammonium lumber, shingles fungicide/insecticide Terephthalates Phthalate New uses of a Estrogenic activity not replacement for chemical approved completely ameliorated plastics containing for poly-terephthalate in some plastics. DEHP and bisphenol (PET) plastics A PBDE flame High volume, high Several on Some toxic, many “no retardant exposure chemicals Department of information/insufficient replacements Ecology’s PBT list. information”

    

87              d. Sediment Quality Sediments are particulates that can be transported by fluid flow and that settle on the bottom of the marine environment. Non-water-soluble contaminants frequently bind to floating clay or silt then deposit in the sediment layer. The sediment layer can therefore document ongoing or past dumping of chemicals into the ecosystem. Numerous plants and animals inhabit, feed from, and grow on the sediment layer of the marine floor. Deposition of toxins within the sediments can result in consumption and bioaccumulation within wildlife, and re-suspension within the water column after disturbance (Gardiner and Hardy 1992, Ferraro and Cole 2002). Existing Monitoring. TBA Proposed Monitoring. Monitoring the concentrations of petroleum derived hydrocarbons in sediments can serve as a baseline for these contaminants in the event of chronic oil pollution or major oil spills that impact intertidal and shallow subtidal habitats. While spilled oil coats rock surfaces, and can often be removed, it also penetrates soft sediments and continues to do damage for many decades.

Although it is less challenging technically to sample and test water, toxics accumulate (and can be more persistent) in fine sediments and aquatic animals. Sampling sediments and animals helps captures short-term events (toxic “spikes”) and compensates for low or highly variable contaminant concentrations over time. Reliability is increased, and sampling frequency can be decreased. Direct causal connection between water-borne contaminants and the food chain can be demonstrated. A sufficiently locally widespread animal model must be selected, preferably one with known accumulation rates for major groups of toxic compounds such as that for the common blue mussel, Mytilus edulis. Barsh, Bell and Harper are currently surveying and screening candidate aquatic species. Collecting and freezing soft sediment cores now, in anticipation of an oil spill or other major contaminating event, would give some baseline information on these chemicals.

   

88  

5.4 Fresh water inputs to the nearshore zone

Regionally, fresh water input from streams has been decreasing during summer and fall months (May-October) in Puget Sound, and increasing in March and April (PSAT 2007, PSS 2011) over the past half century. Snowmelt is earlier, snowpack is lower, and total stream flow was also reduced by 13 percent over that time period. These changes are consistent with the observed rate of atmospheric warming and are predicted to continue. Within the MSA, reduced stream flows throughout the Puget Sound Region will affect surface salinities, and sediment transport from the Fraser River to our north.

Locally, fresh water inputs come from small streams, land runoff, and sewage treatment outfalls (Armstrong et al. 1980). These local sources of pollutants should be monitored regularly, especially near the more urban areas of the MSA. There is an existing program of stream water quality monitoring, in collaboration with the San Juan county schools and the San Juan Nature Institute.

SJC is responsible for monitoring sewage treatment plant outfalls, and will be developing a monitoring program for stormwater outfalls as part of the Critical Areas Ordinance requirements under the Washington State Growth Management Act (SJC, BAS 2007).

5.5 Desalinization plant outflows RO (reverse osmosis) desalination (desal) plants are the type presently in use and being proposed in San Juan County and most parts of the world. The literature is useful but is an incomplete guide to probable impacts of desal plants, because studies are with organisms and habitats other than those in San Juan County and concern desal plants with greater capacity and effluent volume. Procedures and equipment in RO desalination varies and those differences may produce different impacts. Impacts are expected to be less where brine is rapidly dispersed by currents or waves (Höpner and Windelberg 1996; Höpner 1999). None of the sites in San Juan County have constant mixing by waves, as occurs on open coasts. Wind is variable. At some sites fast tidal currents provide mixing that can be very rapid but that can also vary during a tidal cycle.

Potential sources of impacts that have been noted (Einav et al. 2002, Tularum & Ilahee 2007, Lattemann and Höpner 2008, Malcangio and Petrillo 2010, Meneses et al. 2010, Hodges et al. 2011) include: discharge of brine to receiving waters, chemicals used in pre- and post-treatment of water, impingement of larger animals on screens at the intake pipe, noise from pumps, entrainment of animals at the intake pipe, energy required for pumps, leaking of brine from pipes into groundwater, and installation of the desal plant. The chemicals used differ among desal plants, may change over time, and cannot be identified in the case of some proprietary products.

Chemicals that have been used in RO desal plants (not necessarily in the County) include those used to overcome chemical scaling from impurities in the water and biological growth and clogging of the membranes: sodium hypochlorite or chlorine prevents growth of organisms;

89 ferric or aluminum chloride may be added for flocculation to form larger masses that are easier to remove by filters and removal of suspended matter; sulfuric or hydrochloric acid may be added for pH adjustment; sodium bisulfite to neutralize remaining chlorine; polymaleic acid and phosphonates are typical scale inhibitors. Chemicals are also used in cleaning membranes (which can be enzymes to remove bacterial slimes, detergents, biocides to kill bacteria, chelators such as EDTA to remove scale, acids to dissolve inorganics, and caustics to dissolve organic material and silica). With on site cleaning, most of the cleaning chemicals are washed into the brine which is discharged into the marine environment. Information from the operators of desalination plants in San Juan County indicates several procedures that can minimize impacts of cleaning chemicals and thereby affect needs for monitoring. (1) Off-site cleaning of membranes could be required. (2) If there is on-site cleaning, a requirement for chemicals used in cleaning to be known to be harmless. Of chemicals used for cleaning membranes, acid and alkaline treatments (low and high pH) can be rendered not toxic from pH effects if pH is subsequently adjusted before the cleaners are discharged, but some cleaners are proprietary mixes of unknown composition. The second requirement would eliminate on site use of proprietary cleaners of unknown composition. Operators prefer hydrochoric acid to sulfuric acid because it is gentler on equipment and because the chloride present after neutralizing the acid is already present in seawater at a high concentration (D. Drahn, personal communication).

The MSDS (material safety data sheet) for polymaleic acid (a scale inhibitor) says that it is no more than slightly toxic if absorbed or swallowed, that it is moderately irritating to eyes and skin, and that significant health effects are not expected if less than a mouthful is swallowed (indicating low toxicity for this scale inhibitor). Some cleaners also occur in household products. These are enzymes that remove bacterial slimes, biocides that kill bacteria, and detergents. These cleaners are therefore part of a more extensive environmental and regulatory issue. Quantities used in desal plants could be evaluated in relation to quantities entering the sea from other sources and any effects from those other sources.

The EDTA that removes scale occurs in household products. It is a chelator of divalent positive ions. EDTA is a component of algal culture medium and thus is introduced to cultures of marine larvae at low concentrations with no known ill effects. The MSDS indicates (for health effects) that EDTA is a mild irritant. Flocculents are generally used in very large plants that remove the material and dispose of it in land fills (D. Drahn, personal communication). There is also a "pickling" process for keeping membranes when they are not in use. The chemical is sodium metabisulfite and may not present problems of toxicity in the concentrations discharged. The MSDS for sodium metabisulfite indicates irritation to eyes or skin and recommends dilution as the treatment, with no known or anticipated mutagenic effect. Toxicity at low concentrations is not expected.

The impacts of desalinization should also be considered via the whole water cycle, since water is the agent moving nutrients, toxics and pathogens; what happens to the fresh water produced, as well as the brine? Also, this technology enables housing to be built in locations previously not possible (densification), which affects land use, overwater structures and boat traffic.

Existing Monitoring. None at present. There have been a few observations in San Juan County. Megan Dethier (unpublished observation) found no apparent change in sea life on rocks near a desalination plant outfall on Haro Strait, where tidal currents are fast and mixing is rapid. Two studies in the San Juan Islands, following installation of desalination plants, indicated rapid mixing of water near the discharge pipes. In each case salinities were reduced to concentrations near or not detectably different from that of the surrounding water within a few feet of the discharge pipe. A discharge into Griffin Bay near San Juan Island is described in Mayo (2009, The Current Status of Desalination Systems in San Juan County, Washington, and Issues Impacting Their Use, Appendix 4, communicated by Dan Drahn and Chris Betcher). The mixing occurred in slow currents (speeds of 0 to 3 feet per minute). The volume flow of discharged water was unstated. At a discharge into Lopez Sound, measurements indicated rapid mixing to salinities near that of the receiving water; the volume flow of effluent and the current velocities in the receiving water were unstated (Andrew Evers, personal communication).

Proposed Monitoring should include information on characteristics of the desal plants, including the volume of brine discharged per time, salinity of the brine produced (in part dependent on mixture of seawater with brine before discharge), type and position of diffuser at the outfall, characteristics of intake screens or filters and their flushing, chemicals used in operation that enter discharged water, chemicals from cleaning membranes that enter the effluent. Published recommendations for monitoring (e.g., Palomar and Losada 2010) are often for desal plants larger than those presently existing in San Juan County. For plants that pump small volumes and that send membranes off-site for cleaning, a primary concern may be effectiveness of mixing of the discharged effluent. Also, for plants on a small bay, the volume pumped per time relative to the volume of the bay is an indication of impacts from impingement and entrainment at the intake. Useful information on a site includes bottom topography and currents at the outfall. Reported currents should be relevant to the outfall site and include currents at times of slack water on calm days.

A general requirement after installation could be measurement of salinities at and near the outfall when currents in the receiving water are minimal to assess mixing of discharged water. That would create a data base that would aid improved design for outfalls from future desal plants. Monitoring salinity indicates extent of elevated salinities in the receiving habitat. Dye releases may aid in indicating flow of discharged effluent. Measurement of current velocities, especially at minimal flow from wind and tide, may also be useful. In an extreme situation, in which brine sinks to the bottom and forms a stable layer that retards mixing, bottom water and sediments would become hypoxic or anoxic (as occurs naturally in some basins, such as Saanich Inlet). Where such accumulation is suspected, monitoring of oxygen will indicate impacts, as would monitoring of sulfide in sediments. Sediment cores will show the level at which black anoxic sediment occurs. Impingement could be monitored at the intake.

Entrainment can be estimated from volume pumped and concentrations of larvae or other animals likely to be entrained, and the same may be true for impingement. Where volumes pumped are low, the losses from entrainment and impingement will also be low. Where intakes and outfalls are in a small bay, the volume of water in the bay below MLLW and the intertidal volume can be estimated from a chart. If the size, location, design, and operation of a desal plant

91 indicates that effects on benthic plants and animals should be assessed, then monitoring should, if possible, include estimating abundances of species at sites near the effluent discharge and control (reference) sites both before the desal plant is in operation and for several years during operation.

A potential impact that should be examined in San Juan County is possible effects of effluent on movements of fish, even in tidal channels. In a study by Raventos et al. (2006), some fish, instead of avoiding the discharge site, aggregated near the discharge pipe, as can happen at artificial reefs. In a laboratory study with artificial seawater, Iso et al. (1994) observed that juvenile sea bream spent less time in water at high salinities. Would juvenile salmon or other fish moving along shore avoid effluents likely to be in discharged in San Juan County, even with well mixed discharges?

In addition to field monitoring, samples of effluent water, with different degrees of mixing, can be tested in the laboratory for effects on development and behavior. In laboratory experiments, sublethal effects that are likely to decrease survival in the field are of greater relevance than directly lethal effects, because sublethal effects can occur with less concentrated brine. One difficulty in detecting impacts of desal plants in San Juan County is that the plants are small but will likely be numerous. Thus, impacts may be cumulative but not large at any one site; monitoring at any one plant should be capable of detecting small effects. It may not be feasible or efficient to sample large numbers of small installations, but instead to monitor the larger ones and a few of the smaller.

5.6. Oil Spills (Threat No. 1., High & Threat No. 144, Medium) a. Monitoring chronic oil contamination.

Chronic oil contamination occurs continuously, originating from street runoff, marinas, illegal dumping, and private property. Some monitoring occurs via analysis of runoff and sampling within harbors, but there is no monitoring of individual events unless they are severe. Limited data are available for the SJC MSA (WDOE; Coots 1999, Serdar et al. 2001). b. Monitoring large oil spills once they occur

Large oils spills are a real threat along much of the southern and eastern shores of the MSA, because these shores border the routes taken by tankers traveling to and from the Cherry Pt. oil refinery in Anacortes. There have been substantial spills in the Puget Sound region (Chia 1971, MacLeod et al. 1976ab, Clark et al. 1978, Vanderhorst et al. 1979, Brown et al. 1981, Getter and Hayes 1981, Carney and Kvitek 1990, Strand et al. 1990, 1992, Dethier 1991, Reichert 2005, PSAT 2007, PSS 2011), though the MSA area has been fortunate so far. The presence of a rescue tugboat in the Strait of Juan de Fuca, now funded year-round, is an extremely important protective factor for the MSA. Once a large spill occurs, the cleanup is expensive and it takes many decades for intertidal and shallow subtidal communities to recover (e.g. Exxon Valdez spill in Alaska; Paine et al. 1996, Coats et al. 1999, Skalski et al. 2001, Peterson et al. 2003).

92 Oil-derived hydrocarbons stay in sediments for decades, as well (Anderson et al. 1978, 1983, Gundlach et al. 1983, Clifton et al. 1984, Collier 1994).

Proposed Monitoring and Response. Some response and monitoring items suggested include (B. Cowan, IOSA, pers. comm.), communication with the public and other organizations if a spill occurs, sediment analysis for PAHs (establish a baseline presence of oil, archive samples) in various locations updated periodically to document impacts and guide potential clean up and restoration funding, develop a dispersant policy (dispersants are a last ditch effort to control a spill--they cause the oil to sink and disperse through the water column and are themselves toxic), and train a couple of MRC members with strong science and local knowledge in oil spill response so they can work with the state and federal teams. There is also a need to identify “sacrifice” bays or shorelines where oil could be directed to protect more critical habitat.

Ultraviolet absorbance of seawater is a convenient, low cost early warning for organic contaminants from oil spills. For example, BP/Horizon oil spill monitoring uses more sensitive fluorometers to measure crude oil levels in seawater in real time (NOAA oil spill response, 2010).

Dispersants are not recommended for shallow and enclosed areas and can increase damage from spills in some conditions. Booms are recommended to exclude or divert oil at many of the smaller bays. Shores with sediments and low waves, slow currents have priority for protection. There is some consideration of wind directions, but wind can come from a wide variety of directions in the San Juan Islands. Oil would move with the wind to a great extent in many areas and the usual wind directions would be a poor guide at many times. The MRC was surprised there was no planned boom at some sites, such as the bay at the inner end of Eastsound (Ship Bay), but maybe someone predicted that oil won't get that far into East Sound. There are big vulnerable stretches of shoreline that apparently cannot be protected. Examples would be Griffin Bay (with known intertidal spawning sites), the long beaches on Waldron, Is. etc. The shores around the many bird nesting small islands (most of the National Wildlife Sanctuary islets) apparently cannot be protected.

5.7 Nutrients and Pathogens (Threat No. 6, 7 Medium)

The following contaminants are generally not being monitored regularly within the MSA. Information on monitoring programs throughout the Puget Sound Region can be found in the PSAMP 2007 Update (PSAT 2007, PSS 2011). a. Nutrients and Eutrophication

Nutrient loading occurs when nutrients (e.g. phosphate, nitrate, nitrite, ammonium, silicon, iron) enter a particular marine system, then affect the ecological processes occurring therein. A certain amount of nutrient input from streams, rivers, and runoff is normal and can be absorbed by the system. Nutrients also come from ocean water entering the PSR, usually in a deep layer. Excess nutrient loading can cause increases in algal populations, primary production, macroalgae biomass, sedimentation of organic carbon, harmful algal blooms and changes in the makeup of the phytoplankton community (Bernhard et al. 1993, Bernhard 1995). These effects can have further indirect effects producing changes in the benthic biota, reduction in plant biomass, reduced water transparency, changes in sediment biogeochemistry, reduced dissolved oxygen,

93 and which can result in direct mortality of fish and invertebrates, and in food web structure (Ruesink et al. 2003). Eutrophication occurs when nutrient concentrations build up to levels where negative changes in water quality , oxygen and biotic composition occur; areas most sensitive to eutrophication are those with high local input of nutrients, low flushing rates, strong stratification, and the potential for decreased oxygen concentration (PSAMP 2007, Table 5-1 WDOE).

Existing Monitoring. WDOE monitors nutrients and dissolved oxygen at one site within the MSA, Eastsound on Orcas Island, one just north of the MSA, one at the southern boundary of the MSA (JEMS station), and at many sites to the east and south of the MSA, covering most of the Puget Sound Region. Low dissolved oxygen has been detected in Hood Canal and to the east of Whidbey Island (PSAMP 2007, Fig. l5-4) and ammonia is generally high at sites in southern and central Puget Sound, and in Bellingham Bay and Eastsound, Orcas Island (PSAMP 2007, Fig. 5- 5). UW FHL researchers monitor nutrients and dissolved oxygen at two stations in San Juan Channel during October-December of each year (Pelagic Ecosystems Research Apprenticeship), and would like to continue this monitoring throughout the year.

Proposed Monitoring: NA

b. Pathogens and Biotoxins

Pathogens in marine waters come from a variety of sources including animal and human wastes. These include disease-causing microorganisms such as viruses, protozoans, and bacteria. Risks to humans include respiratory, skin, eye and ear infections, norovirus-related gastrointestinal disease, bacterial gastroenteritis (Vibrio), paralytic shellfish poisoning (PSP, biotoxin) (Jonas- Davies and Liston 1985), meningitis and hepatitis. Biotoxins are produced by algae and accumulate in shellfish and other marine biota. PSP comes from Alexandrium catenella phytoplankton, and causes closures of shellfish beds in the PSR. Another toxin, domoic acid, has caused closures of razor clam beds on the outer coast of Washington, but has not yet entered the PSR (Homer et al. 1996, Wekell et al. 2000). This toxin is produced by dinoflagellates (Pseudo- nitschia spp.), and is the cause of amnesic shellfish poisoning (ASP). Biotoxins have also caused mortality of sea birds and marine mammals along the west coast (Lowenstine 2004). Another group of pathogens affects marine animals directly, especially marine mammals; these pathogens include protozoans (Toxoplasma), marine distemper virus, cetacean morbillivirus, canine distemper virus and others (Gaydos et al. 2004). Numerous other pathogens affect fish (e.g. gill parasites) and limit their population growth.

Existing Monitoring: Fecal coliform bacteria are used as easy-to-measure indicators of the possible presence of other pathogens that come from human or animal wastes. WDOH monitors water quality over shellfish beds throughout the PSR. Within the MSA, there are 10 stations monitored by WDOH, and only two of those have shown some evidence of fecal pollution (PSAMP 2007, Figure 5-7 to 5-11), in the “fair” category. Coastal sites to the northeast of the MSA, and directly south, have much higher coliform counts, often in the “bad-fair” category and many of those sites show an increasing trend. Beach monitoring, for swimmer safety, is also carried out by WDOE (BEACH Program) although none of those sites are in or adjacent to the MSA. Coastal beaches from the far northern to the far southern limits of Puget Sound show some excedence of bacterial counts and beach closures. The total number of closures due to sewage

94 spills has increased from 2003 on, possibly due to better detection and communication rather than more spills alone (PSAMP 2007, Figs. 5-13 to 5-14).

For information on state controls: TMDL Process Overview, 303(d) Listings, Point Sources and NPDES Permits (see PSAMP 2007, Ch. 8)

Proposed Monitoring: as outlined above

5.8 Land Use (Threat No. 3, High & Threat No. 16, Low) a. Changes in land cover, vegetation, impervious surfaces etc. Historical photographs provide the opportunity to examine changes in land cover, vegation and surface types over almost a century, although the coverage of different island areas is spotty and incomplete. The high resolution, infra-red aerial photo set (2004 and 2006) for all of San Juan County conducted for the bull kelp surveys also provides a baseline data set that can be used for future analysis of shoreline or upland land cover. See also: Shull and Bulthius (2001), Wyllie- Echeverria et al. (2004a). LIDAR surveys being conducted in 2011 and later will be particularly useful for this purpose. b. Background- Shoreline Land Use Studies While much scientific research has been conducted along our shorelines similar attention has not been paid to understanding the effectiveness of regulations or the cumulative impacts of incremental development.

Friends of the San Juans Analysis of Shoreline Permit Activity for San Juan County, 1972-2005. The FRIENDS analysis of shoreline permit activity completed the first spatially and temporally explicit analysis of permit activity on shoreline parcels in the county. Total shoreline permit activity was analyzed for the following project activity types: aquaculture, barge, beach access, boat house, boat ramp, bulkhead, clearing and grading, dock, guesthouse, logging, marine railway, mooring buoy, setback, shoreline, stormwater and transient rental. Permit activity was also characterized by permit type, including substantial development, exemptions and code investigations. Shoreline building permit activity from 1992 to 2005 was also included. Results provide an objective basis for understanding shoreline permit activity trends and conducting an initial analysis of shoreline policy effectiveness. It is important to remember that the analysis is based on the county’s permit database, and is not necessarily an accurate reflection of on-the- ground conditions, but of trends in permit activity but it does provide a basis for developing a cumulative impact analysis.

San Juan Initiative Case Studies. Through its case study approach, the San Juan Initiative recently (early spring 2008) documented shoreline modifications including armoring, docks, and marine riparian vegetation conditions for four case study areas within San Juan County through aerial photo interpretation and field-based inventory. Change in vegetation within the 200 ft. shoreline jurisdiction was also assessed using historic (need to check which set ‘76?) and recent aerial photographs. This approach could be expanded to other areas to monitor changes in shoreline vegetation in the shoreline (SJI 2008). See also: (Bookheim et al. 2002)

Existing Monitoring. NA

95 Proposed Monitoring. Shoreline vegetation. An understanding of change over time in shoreline vegetation type, cover and overhanging vegetation would inform understanding of policy effectiveness and also provide critical information for a cumulative impact assessment of land use and nearshore habitat. This type of monitoring can be conducted using existing vertical (FSJ, SJC) and oblique (WA Ecology) aerial photo data sets for different time periods. LIDAR surveys being conducted in 2011 and afterward will also assist in this process.

To improve understanding of the impacts of shoreline modifications, a comprehensive field inventory of modifications is needed to provide a baseline data set. This may exist for overwater structures (recent DNR mapping effort) but is not yet available locally and has not been completed for other structures such as bulkheads, beach access, boat ramps etc. Spatially explicit data is available for permitted structures with a record in the SJC permit database, but this data set is not an accurate reflection of on-the-ground conditions. The SJC permit database should be updated to include a searchable field for project activity type (e.g. dock, barge landing etc.). Currently, the database is only searchable by parcel number or landowner name, which does not support understanding of land use patterns.

c. Shoreline hardening, armoring

Shoreline hardening or armoring occurs when natural erosion threatens buildings, roads or other structures close to the shore. While such measures may halt erosion temporarily, they also change the flow of sediment to and along the shore, and modify habitat quality for a number of species (Airoldi et al. 2005). Because such structures need permits, it is theoretically possible to keep track of changes over time for each shoreline segment. However, recent surveys have shown that this is not the case, either because permits were not utilized or because changes were made at undetermined times in the past (San Juan Initiative 2008). Future monitoring may be more tractable as the county finds ways to better track permits, and discover modifications made without permits. d. Changes in forest cover (logging, land use change)

Changes in forest cover have been occurring for more than a century, and the San Juan Archipelago is no exception. Forests were converted to fields and farmland, some of which has gone back to forest or has been developed for more urban or suburban uses. With such changes comes increased runoff, especially where impervious surfaces are installed. Expected population increase in the county will result in additional conversion of land, although there is a strong movement to purchase and conserve undeveloped land. Monitoring of changes in land use is conducted by the county, and is part of the CAO and SMP processes. e. Changes in freshwater and marine riparian vegetation

Freshwater riparian vegetation (vegetation along waterways) serves the important ecosystem function of removing nutrients from groundwater before they end up in streams, rivers, ponds and lakes, and ultimately in the coastal ocean (Brennan et al. 2004). This vegetation also provides habitat for birds and other species that prefer ecotonal (edge) habitats. Along coastal beaches, marine riparian vegetation performs another newly discovered function; shading from overhanging trees cools intertidal habitats, which may help benthic species survive periods of intense insolation, but which definitely helps fish eggs (smelt, Rice 2007) survive and produce

96 young. Monitoring of riparian vegetation is not currently happening, except for trees at building sites. Proposed monitoring would include aerial surveys and ground-based verification along selected streams, wetlands, and shorelines. f. Impervious surfaces (roads, parking lots, driveways)

Impervious surfaces allow more pollutants to be delivered to streams, rivers, and marine waters, because there is no chance for such water to be filtered through soil and vegetation (see riparian vegetation above). Instead, oil, fertilizer, pesticides, and many other contaminants travel directly from roads to stormwater drainage pipes and channels, and directly into the water. It is very clear that regions with higher percentages of impervious surface have more pollution in adjacent waterways, and show major changes in stream biota. At present, San Juan County has a very low percentage of impervious surfaces, and negative effects are most likely to be seen in Friday Harbor and a few other sites with dense population and more impervious surfaces. Monitoring the area of impervious surface in the county is currently done by the state. Monitoring stormwater runoff provides one way to determine if impervious surfaces are allowing substantial pollutants to reach the water. Runoff will be monitored as part of the county’s new stormwater monitoring program (Stillwater 2010) to be initiated in 2011.

6. Overwater Structures (Threat No. 3, High)

5.9 Docks, marinas and other structures

Several studies of effects of docks on eelgrass have been conducted by WDFW in San Juan County. The data indicate reduction of eelgrass at some docks, not at others, but the studies in general have lacked statistical power (Fresh et al. 2006). Information provided from any future monitoring will enhanced by a BACI (Before-After, Control-Impact) sampling design with enough samples for a predetermined desired power. Shading is the most easily documented effect of a single dock (Fresh et al. 2006), but effects may extend beyond shading, and effects of shade may affect organisms in addition to eelgrass (Cardwell and Koons 1981). Mitigation has been tried in other localities in the PSR (Cheney et al. 1994). Positive effects of hard structures should also be considered including refuges for juvenile fish, and establishment of kelp and other algal populations in areas with limited hard substrata.

Existing Monitoring. See PSNERP’s Change Analysis dataset.

Proposed Monitoring. The practical limits on duration of monitoring could result in some impacts of docks being missed. A supplementary form of monitoring for impacts would be a retrospective survey of existing docks, with data on distribution and abundance of eelgrass or other selected organisms under and at distances from docks; data on the dock age, size, design and orientation; data on water depth; and (so far as interviews can indicate) data on boats and boat use.

Cumulative effects of many scattered docks are more difficult to monitor and demonstrate than impacts from large concentrations of docks and boats because the effects are more gradual and widespread and adequate sites for comparison less likely to be available. Litter such as plastic sheets creates anaerobic patches on the bottom. Some toxic materials that are associated with use

97 of boats enter the water and can reduce survival of marine organisms when in low concentrations.

Treated woods approved for marine construction can release toxic metals. Floats can act as floating breakwaters, changing deposition of sediments along the shore. There can also be indirect biological effects. Docks contribute shell debris to the sediments below and provide a habitat for some crabs and seastars that prey on other organisms in the vicinity, thereby extending the area of disturbance. Data are needed to indicate the magnitude of these or other effects. b. Mooring buoys, DNR. Coastal Geologic Services recently conducted a detailed analysis of dock, pier and float structures for four small case study areas as part of the San Juan Initiative (CGS 2008). This was done using a combination of aerial photography and field analysis and could be used as a basis for future, expanded efforts. In addition, WDNR has digitized docks in all of Puget Sound (WDNR 2005). Permitted docks in SJC have been mapped through the FSJ shoreline permit analysis (FSJ 2008). Of an estimated 5000-8000 buoys, only 200-300 were found to be DNR registered. (note: those over 2 yrs old not required to register). Most are not the correct design to minimize damage to seagrass and other benthos (Betcher and Williams 2005). (See also David Roberts, WDNR in Sedro Wooley, for a recent complete mooring buoy survey)

5.10 Boat traffic, effects on marine mammals, others (Threat No. 0, High)

Boat traffic around marine mammals is known to affect their behavior, and the presence of the Southern Resident Killer Whales (orcas) in the MSA for much of each year attracts a great deal of boat traffic (NOAA 2010). Compared to the Northern Resident population, which has been increasing steadily since the 1970s, the Southern Residents have had both periods of increase, and of decrease (EPA 2006). Orcas have been killed by encounters with boats in the Puget Sound Region, and this may contribute to the unexplained mortality events within this population. Boat wakes also affect intertidal communities in areas not normally exposed to heavy wave action (Nyblade 1979, Guedelhofer and Murdoch 2000).

5.11 Non-indigenous species (NIS): Nuisance species, others (Threat No. 5, Medium)

Invasive marine species have been documented in the Puget Sound region for several decades (Byers 2002, 2005, Secord 2003, 2004ab, Wonham and Carlton 2005), including those discovered during broad-scale surveys by taxonomic experts (Mills et al. 2000, Cohen et al. 2001, Copping and Mark 2004). Klinger et al. (2006) noted higher abundances of two invasive species in reserves within the MSA. A number of non-indigenous ascidians have become common on pilings, docks, and in certain rocky subtidal areas (Mills et al. 2000, Cohen et al. 1998, 2001), but are very rarely seen in rocky subtidal communities (Sebens, Elahi. pers. obs.).

The European green crab (Carcinus maenas) is now found on the outer coast (e.g. Willapa Bay, Dumbauld and Kauffman 1998, Jamieson et al. 1998, McDonald et al. 1998, 2001, 2003, 2004, Carr and Dumbauld 2000, Jensen et al. 2000, 2002) but has not made it to the San Juan Archipelago yet. It consumes young shellfish, and is a serious problem on the east coast of North America. WDFW started a program in 1999 to monitor green crabs; currently only volunteers do these surveys (Ann Eissinger pers. comm.). Beginning in late 2007, new program funded by

98 WDFW that uses trained volunteers to search for 32 invasive species (from plants to macroalgae to invertebrates).

Existing Monitoring. TBA (Note: Is there still monitoring of the ongoing threat of Spartina anglica? It was eradicated from Argyle, but are people watching for other infestations?)

Proposed Monitoring. Monitoring to determine the spread of established NIS: Several species of NIS already established within SJC are highly likely to persist and spread. Among these are the seaweed Sargassum muticum (Giver 1999), the seagrass Zostera japonica, the Varnish clam (Mills 2002) Nutallia obscurata, the mud snail Batillaria attrementarium, the Pacific oyster, Crassostrea gigas, and several non-native tunicate species. At least some of these are known to have negative impacts on local marine communities. The distribution of Sargassum might be estimated from aerial photos in a few habitats, but the distribution and spread of other NIS will require field sampling.

Monitoring to detect new invasions: NIS are likely to invade rocky, soft-sediment, and engineered habitats. Systematic monitoring to detect new invasions will be difficult, because predictability is low. Consequently, opportunistic monitoring performed in the course of regular monitoring of sites for other purposes might be the most cost-effective means of detecting new invasions. Collaborations between volunteer groups, and experts at UW FHL who can identify newly invasive species, would be a good use of resources.

Aquaculture presents threats from disease, eutrophication, and escapes. In this region we must consider fish aquaculture, mollusk aquaculture, and potentially others (e.g. seaweeds such as the kelp Undaria pennitifida). Aquaculture can introduce non-native species to the local environment (Simenstad and Fresh 1995). The target species (or species under culture) can escape directly (e.g. oysters, fish, other) or the species can disperse via larvae (e.g. shellfish) or through intentional or unintentional human transport. Associated diseases and parasites can be spread from farms by similar means. Monitoring for escapees, disease, and parasites might best be performed opportunistically. Alternatively, the county could require regular monitoring to be performed by the applicant as a requirement of new aquaculture permit applications. (Megan Dethier noted several new worm parasites found recently, pers. comm.).

Aquaculture of both native and exotic species is well established in the Salish Sea/PSR, including geoducks (Goodwin 1976, Goodwynn 1977, Beattie 1988, 1992ab, 1998, Pease and Cooper 1988, Bradbury 1989, Goodwin and Pease 1989, Beattie and Goodwin 1992, Beattie et al. 1995, Bradbury et al. 2000, Heizer 2000, Sizemore 2000, Johnson et al. 2004), other clams (Goodwin 1972, 1977, 1978, Ellifrit et al. 1973, Goodwin and Shaul 1978, Bourne 1982, 1998, Chew 1988, Palacios and Armstrong 1989, Harbo and Bourne 1992, Campbell and Cahalan 1996, Cook 1996, Dumbauld et al. 1996, Sterritt et al. 1996, Wood 1996, Bourne and Heritage 1997, Davis 1998, Gillespie et al. 1998, Heath 1998, Kronlund et al. 1998, Child and Campbell 2000, Palacios et al. 2000, Caffey et al. 2001, Stanley and Gregg 2004, Whitney and Wildermuth 2004,), mussels (Heritage 1981, Skidmore and Chew 1985, Skidmore et al. 1985, Ruckelshaus et al. 1993,) and Asian oysters (Clark and Chew 1976, Scholz et al. 1985, Davis 1988, Dumbauld et al. 1997, 2000a, 2001ab, Cheney et al. 1998, 2001ab, Heath and Bourne 1998, Ruesink 1998, 2007, Dumbauld 2002, Friedman et al. 2003, Hosack et al. 2004, Trimble et al. 2005).

5.12 Threats from fishing/harvesting, historical fishing, derelict fishing gear, and predation by marine mammals

(Threat No. 10 Medium, Threat No. 12 Medium, Threat #13 Medium, Threat #9 Medium)

Clearly, the declines in salmon within the MSA are the result of a number of impacts over a broad geographic scale, including historical fishing, dammed rivers, changed land use, toxic chemicals, and other factors. Rockfish in the MSA have been impacted mostly by historical fishing, and have been very slow to recover (PSAT 2007, PSS 2011) because of slow growth and recruitment, and great longevity. Derelict fishing gear is more common in the MSA than in the rest of the Puget Sound Region and continues to claim many victims, although it is being removed fairly rapidly. Predation by marine mammals is a significant mortality factor for salmonids (e.g. orcas) and groundfish (e.g. harbor seals) and probably for many benthic invertebrate species as well, and is an expected component of a healthy ecosystem. Lack of predation on sea urchins, because their mammal predators are currently missing (sea otters, Carter and VanBlaricom 2002, Carter et al. 2007) is also affecting their population densities, although historic harvesting has kept their numbers low for several decades within the MSA.

100 Section 7. Monitoring, Implementation, and Adaptive Management

7.1 Overview. One of the main goals of any monitoring plan is to determine whether actions taken to mitigate some aspect of environmental degradation are having the desired effect. The MSA monitoring plan is designed to do this as well. Specifically, the MSA Plan (2007) sets out a list of benchmarks, which are goals for the MSA, along with strategies to achieve those goals, and targets for study and for management. The monitoring program addresses these targets, and in some cases adds or targets that were not covered in the MSA Plan or broadens the definition of such targets.

Another goal of a monitoring program is to determine if biotic communities are changing with time, whether or not they are responding to the particular management strategies implemented. In some cases, global climate change may have such a strong effect on a particular species that mitigation strategies are unlikely to function as desired. Once we have that information, those strategies can be changed or discarded. Furthermore, we may find that other species (non-target) are showing greater change than expected, either negatively or positively. For example, a new species may show up in the area and begin to replace species already here. Although this new species was not a target, it clearly must become one in an adaptive management plan.

7.2. Draft Strategies (from MSA Plan 2007). Following the development of benchmarks, the Marine Resources Committee identified a comprehensive list of strategies. Strategies are management actions that will directly address the top priority threats in order to achieve the benchmarks. The MRC developed the draft strategies list working from proposals put forward by stakeholders and managers at the Threat Assessment Workshop and Second Managers Work Session. In addition, the Core Team developed a situation analysis for each target. These are diagrams that draw out the connections between the target, the stresses to that target and the human activities that are causing the stress, providing a useful tool for identifying the most effective strategies.

For an example of a situation analysis diagram, please see Appendix F (MSA Plan 2007). Draft strategies are presented by Target under the benchmark they are aiming to achieve. “B” is for biodiversity benchmarks; “T” is for threat-based benchmarks; “SC” is for Socio Cultural benchmarks. Many of the benchmarks are listed multiple times because they apply to more than one target. Please refer to the strategies matrix (MSA Plan 2007, Appendix G) to better understand the relationships between the targets, benchmarks, strategies and threats. Criteria for the strategies are that they are : 1. MRC’s job: within our mission, authority, and ability; and are not being done by another group., 2. Smart: most effective/ greatest impact, 3. Start-ups: can occur within five years.

7.3 Benchmarks and strategies presented by target. For a matrix of benchmarks, strategies and associated threats, see MSA Plan, Appendix E.

Conservation Target: Nearshore sand, mud and gravel communities.

Benchmark B-4. The regional coverage of eelgrass (Zostera marina) remains stable on beaches and increases by 10 percent in embayments over a 5-year period by 2013. Strategies: 1. Recommend improved and coordinated policies for building, anchoring, docks, enforcement, and mitigation. 2. Improve water quality relative to eelgrass needs (see T-7, strategy 1) 3. Education & outreach on the importance of eelgrass and best marine use/shoreline

101 development practices

Benchmark T-3. Ensure that there are enough salmon of the right sizes and species available within the MSA at the right times of year to support restored marine mammal populations. Strategies: 1. Implement local salmon recovery plan, 2. Connect with regional efforts

Benchmark T-4. Reduce the number of miles of armored shoreline by ___% (or ___ miles) by 2016. Strategies: 1. Minimize new armored shoreline 2. Remove shoreline armoring where appropriate (soft shore blueprint) 3. Education & outreach on the benefits of “softshore”

Benchmark T-5 Reduce chronic and catastrophic oil pollution Strategies 1. Minimize chronic pollution from land and marine sources (includes medium spills and chronic events like bilge pumping.) 2. Support efforts to reduce risk and improve response to oil spills.

Benchmark T-6. Reduce greenhouse gas emissions from San Juan County according to the same standards adopted by Seattle. Strategy: 1. Promote concept of the county doing its part to reduce greenhouse gas emissions (think globally, act locally)

Benchmark T-7. Nitrogen inputs from human sources do not exceed more than 10 percent of natural levels by 2017 – considering changing to capture all pollutants that we care about. Strategy: Draw attention to/include marine issues (stormwater, wastewater, etc) within watershed management plans and programs

Conservation Target: Rocky intertidal and rocky subtidal communities

Benchmark T-2 improved objective for maintaining healthy kelp habitat and community dynamics. Strategy - Still need to develop strategies. Research is a priority.

Benchmark T-5. Reduce chronic and catastrophic oil pollution. Strategies: 1. Minimize chronic pollution from land and marine sources (includes medium spills and chronic events like bilge pumping.) 2. Support efforts to reduce risk and improve response to oil spills.

Benchmark T-6. Reduce greenhouse gas emissions from San Juan County according to the same standards adopted by Seattle. Strategy: Promote concept of the county doing its part to reduce greenhouse gas emissions (think globally, act locally)

Conservation Target: Rockfish, lingcod and greenling

Benchmarks B-1. Increase lingcod populations to greater than 25% of unfished spawning biomass by 2027 and increase rockfish populations to greater than 25% of unfished spawning biomass by 2037. Maintain kelp greenling populations at 2006 levels. T-1. Impacts of harvest activities within the MSA on the rate of rockfish species recovery are within 10% of the time it will take to recover rockfish populations under zero harvest-related mortality by 2037. Strategies: 1. Reduce bycatch of select species.

102 2. Suspend direct harvest of select species until recovery goals are met. 3. Promote public awareness of the status of and threats to rockfish, lingcod, and greenling

Benchmark T-5 Reduce chronic and catastrophic oil pollution. Strategies: 1. Minimize chronic pollution from land and marine sources (includes medium spills and chronic events like bilge pumping.) 2. Support efforts to reduce risk and improve response to oil spills.

Conservation Target: Marine Mammals

Benchmark B-2 Increase the resident killer whale population size to greater than 103 animals by 2020. Strategies: 1. Increase salmon (see T-3), 2. Reduce disturbance 3. Support efforts to reduce bioaccumulative toxins

Benchmark B-3. Restore herring spawning to all historic areas. Strategies: 1. Protect and restore spawning habitat 2. Support regional herring recovery efforts

103

Conservation Target: Pacific Salmon

Benchmark B-3. Restore herring spawning to all historic areas. Strategies: 1. Protect and restore spawning habitat 2. Support regional herring recovery efforts

Benchmark B-4. The regional coverage of eelgrass (Zostera marina) remains stable on beaches and increases by 10 percent in embayments over a 5-year period by 2013. Strategies: 1. Recommend improved and coordinated policies for building, anchoring, docks,enforcement, and mitigation. 2. Improve water quality relative to eelgrass needs (see T-7, strategy 1) 3. Education & outreach on the importance of eelgrass and best marine use/shoreline development practices

Conservation Target: Seabirds

BenchmarkB-3. Restore herring spawning to all historic areas. Strategies: 1. Protect and restore spawning habitat 2. Support regional herring recovery efforts

Benchmark B-5. a) The number of nesting pairs of black oystercatchers remains stable at the 2006 level or increases over a four year timeframe by 2017. b) The number of nesting pairs of pelagic cormorants is stable at the 2006 level or

104 increasing over a four year time frame by 2022. Eagles are a threat with no strategy. Not within our goals to address this threat. Solution is to increase population levels to withstand increased predation. Strategies: 1. Reduce disturbance, 2. Reduce impacts of derelict fishing gear, 3. Reduce oil spill risk (see T-5), 4. Increase prey base (see B-3)

Benchmark T-5 Reduce chronic and catastrophic oil pollution Strategies: 1. Minimize chronic pollution from land and marine sources (includes medium spills and chronic events like bilge pumping.) 2. Support efforts to reduce risk and improve response to oil spills.

Socio-cultural target: Enjoyment of the marine environment

Benchmark SC-1. There are viable recreational, commercial, ceremonial and sustenance fishing opportunities year-round for county residents, tribes with usual and accustomed fishing rights and visitors by 2037. Strategies: 1. Ensure that species restoration/recovery is to a level that allows sustainable fishing. (need to clarify or quantify “sustainable”) 2. Ensure fisheries management supports a local fishing economy.

Benchmark SC-4. Locally-harvested marine species pose insignificant risks to human health, given local rates of consumption, by 2017. Strategies: 1. Promote water quality protection through best management practices. 2. Determine scope and nature of the water quality problem and develop implementation plan.

Benchmark SC-5. In San Juan County, the majority (greater than 50% percent) of people are aware, involved, and feel ownership of the MSA. Strategies: 1. Communicate a clear, inspiring stewardship message to the public. 2. Foster projects that engage the public (seasonal and year-round residents) in marine stewardship, 3. Identify and engage key partners as active marine stewards.

Benchmark SC-6 non consumptive enjoyment benchmark, such as: a scenic, functional and natural marine environment is available for human enjoyment. Strategies: 1. Recommend that county plan for sea level rise and other climate change implications. 2. Recommend that county policies & regulations are directed at achieving this benchmark. 3. Help marine managers address the pressures on marine resources associated with increased population and demand.

105 2. Suspend direct harvest of select species until recovery goals are met. 3. Promote public awareness of the status of and threats to rockfish, lingcod, and greenling.

Benchmark B-3. Restore herring spawning to all historic areas. Strategies: 1. Protect and restore spawning habitat, 2. Support regional herring recovery efforts

Socio-cultural Target: Thriving marine based livelihoods

Benchmark SC-2. By 2017, there is a reliable marine transportation infrastructure with limited and properly sited facilities for vessels with freight movement capacity at all ferry-served islands and access available to transfer passengers from small boats (from other islands) to ferries at all WSF ferry landings. Strategy: 1. Work with county and port districts on criteria for facility sighting, operation and maintenance. (Facility includes barge landings)

106

Benchmark SC-7 Healthy marine environment that sustains thriving marine-based livelihoods. Strategy 1. Incorporate this vision into a communication strategy (A-1).

Benchmark T-7. Nitrogen inputs from human sources do not exceed more than 10 percent of natural levels by 2017 – considering changing to capture all pollutants that we care about. Strategy: Draw attention to/include marine issue (stormwater, wastewater, etc) within watershed management plans and programs.

Socio-cultural target: cultural traditions, ceremonial, subsistence, sustenance and spiritual uses and aspects.

Benchmark SC-3. There is a general acceptance and awareness of marine related cultural practices and traditions, including treaty fishing rights by 2017. Strategies: 1. Continue and build upon MRC, county and others’ outreach efforts with the tribes. 2. Support others’ efforts to highlight traditional marine practices.

Benchmark SC-4. Locally-harvested marine species pose insignificant risks to human health, given local rates of consumption, by 2017. Strategies: 1. Promote water quality protection through best management practices, 2. Determine scope and nature of the water quality problem and develop implementation plan.

All Conservation targets, Socio-cultural targets and all Benchmarks Strategy: Develop a comprehensive communication strategy to deliver our messages to the public

107 References

Airoldi, L., M. Abbiati, and M.W. Beck,. 2005. An Ecological Perspective on the Deployment and Design of Low- crested and Other Hard Coastal Defense Structures. Coastal Engineering. Anderson, J. W., R. G. Riley, and R. M. Bean. 1978. Recruitment of benthic animals as a function of petroleum hydrocarbon concentrations in the sediment. J. Fish. Res. Board Can. 35:776-790. Anderson, J. W., R. G. Riley, S. L. Kiesser, B. L. Thomas, and G. W. Fellingham. 1983. Natural weathering of oil in marine sediments: Tissue contamination and growth of the littleneck clam, Protothaca staminea. CONFERENCE ON POLLUTION IN THE NORTH ATLANTIC OCEAN., 1983, pp. 70-77, Canadian Journal of Fisheries and Aquatic Sciences 40:no. Andrews, J. H. 1977. Observations on the pathology of seaweeds in the Pacific Northwest. Can. J. Bot 55:1019- 1027. Angell, T., and K. C. Balcomb. 1982. Marine birds and mammals of Puget Sound, Washington. Sea Grant Program, University of Washington, Seattle, WA. Armstrong, D. A., C. Rooper, and D. Gunderson. 2003. Estuarine Production of Juvenile Dungeness Crab (Cancer magister) and Contribution to the Oregon-Washington Coastal Fishery. Estuaries 26:1174-1188. Armstrong, J. W., R. M. Thom, and K. K. Chew. 1980. Impact of a combined sewer overflow on the abundance, distribution and community structure of subtidal benthos. Mar. Environ. Res. 4:3-23. Baldwin, B. C., S. B. Yamada, and H. Metcalf. 1992. Predation by the red rock crab Cancer productus: The role of crab density, tide level, and prey size on predation rate. Journal of Shellfish Research [J. SHELLFISH RES.] 11:551 p. Balch, N, D. Brown, R. Pym, E. Marles, D. Ellis, and J. Littlepage. 1975. Monitoring marine outfalls by using ultraviolet absorbance, Journal of the Water Pollution Control Federation, 47 (1), 195-202. Banks, J., and P. Dinnel. 2000. Settlement behavior of Dungeness crab (Cancer magister Dana, 1852) megalopae in the presence of the shore crab, Hemigrapsus (Decapoda, Brachyura). Crustaceana 73:223-234. Barrie, J. V., and R. G. Currie. 1997. Anthropogenic alteration of the natural evolution of the Fraser River Delta, Canada. Centre for Advanced Engineering, University of Canterbury Private Bag 4800 Christchurch New Zealand. Barrie, J. V., and R. G. Currie. 2000. Human Impact on the Sedimentary Regime of the Fraser River Delta, Canada. Journal of Coastal Research 16:747-755. Barry JP, Baxter CH, Sagarin RD, Gilman SE (1995) Climate-related, long-term faunal changes in a California rocky intertidal community. Sci v267:672 Barsh, R., J. Bell, S. Barr, K. Taylor, A. Wilson, and R. Wilbur. 2007. Preliminary Evidence for Phenanthrene, a Polycyclic Aromatic Hydrocarbon (PAH), in Some Batches of Paving Materials Used in San Juan County, WA. KWIÁHT (Center for the Historical Ecology of the Salish Sea), Lopez Island, WA, (unpublished report) Barsh, R., J. Bell, R. Harper, J. Plante, and K. Duong. 2008. Preliminary Survey of Toxic Metals in San Juan County Surface Waters. KWIÁHT (Center for the Historical Ecology of the Salish Sea), Lopez Island, WA (unpublished report) Barsh, R., J. Bell, E. Blaine, G. Ellis, and S. Iverson. 2010. False Bay Creek (San Juan Island, WA) Freshwater Fish and their Prey: Significant Contaminants and their Sources. KWIAHT Report (Center for the Historical Ecology of the Salish Sea), Lopez, Washington, (unpublished report) Beattie, H. 1998. Geoducks and the Washington department of fish and wildlife. Beattie, J. H. 1988. A sand substrate nursery for geoduck clams (Panope abrupta ). Journal of Shellfish Research 7:562. Beattie, J. H. 1992a. Geoduck enhancement in Washington State. Beattie, J. H. 1992b. Geoducks, predators, and volunteers. Journal of Shellfish Research [J. SHELLFISH RES.] 11:551 p. Beattie, J. H., B. Blake, and D. Herren. 1995. Improving survival of planted juveniles of the geoduck clam (Panopea abrupta) using predator exclusion devices. Beattie, J. H., and C. L. Goodwin. 1992. Geoduck culture in Washington state: Reproductive development and spawning. Beaudreau, A. H., and T. E. Essington. 2007. Spatial, temporal, and ontogenetic patterns of predation on rockfishes by lingcod. Transactions of the American Fisheries Society 136:1438-1452. Bell, J., and R. Barsh. 2010. Development and application of a method for the analysis of diethylhexyl phthalate (DEHP) in San Juan County waters. KWIÁHT (Center for

108 the Historical Ecology of the Salish Sea), Lopez, Washington (unpublished report) Bernard, F. R. 1978. British Columbia faunistic survey: subtidal and deepwater megafauna of the Strait of Georgia. Report, Fisheries and Marine Service, Nanaimo, B.C. (Canada). Pac. Biological Station. Bernhard, A. E., P. M. Cassidy, and E. R. Peele. 1993. Nutrient enrichment studies on phytoplankton in Padilla Bay, Northern Puget Sound, Washington. Standard; Conference; Summary. Bernhard, A. E., and E. R. Peele. 1997. Nitrogen limitation of phytoplankton in a shallow embayment in northern Puget Sound. Estuaries 20:759-769. Berry, H., J. Harper, M. Dethier, and M. Morris. 2002. Spatial patterns in shoreline habitats: Results from the ShoreZone inventory of Washington State. Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Berry, H., T., J. Mumford, and P. Dowty. 2005. Using historical data to estimate changes in floating kelp (Nereocystis luetkeana and Macrocystis integrifolia) in Puget Sound, Washington. Proceedings of the 2005 Puget Sound/Georgia Basin Research Conference. Puget Sound Action Team, Olympia, Washington. Berry, H. D., A. Sewell, S. Wyllie-Echeverria, B. Reeves, T. Mumford, J. Skalski, R. Zimmerman, and J. Archer. 2003. Puget Sound submerged vegetation monitoring project: 2000-2002 monitoring report. Pages 60, plus appendices in W. S. D. o. N. R. Nearshore Habitat Program, editor. Bertness, M. D., and D. E. Schneider. 1976. Temperature relations of Puget Sound thaids in reference to their intertidal distribution. Veliger 19:47-58. Blanchette, C. A., P. T. Raimondi, M. Wilson, D. Lohse, A. Kendall, K. Kusic, H. Livingston, E. Maloney, and M. Williams. 2003. Beyond biogeography: Large-scale patterns of distribution and abundance of intertidal marine algae along the US West Coast. Journal of Phycology 39:4. Bookheim, B., H. Berry, and J. Harper. 2002. An inventory of Washington State's marine shorelines using the ShoreZone mapping system. Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Bourne, N. 1982. Distribution, reproduction, and growth of Manila clam, Tapes philippinarum (Adams and Reeves), in British Columbia. Journal of Shellfish Research 2:47-54. Bourne, N. 1983. Clam predation by scoter ducks in the Strait of Georgia, British Columbia. Journal of Shellfish Research 3:84. Bourne, N. 1984. Clam predation by scoter ducks in the Strait of Georgia, British Columbia, Canada. Report 0706- 6457. Bourne, N. F. 1998. Re-examination of Manila clam, Tapes philippinarum, distribution in British Columbia, Canada. World Aquaculture Society, 143 J.M. Parker Coliseum Louisiana State University Baton Rouge LA 70803. Bourne, N. F., and G. D. Heritage. 1997. Intertidal clam surveys in British Columbia - 1992 and 1993. Report 0706- 6457, Department of Fisheries and Oceans, Nanaimo, BC [Canada], Sci. Branch. Bradbury, A. 1989. Survival of hatchery-grown geoduck (Panope abrupta ) seed in Puget Sound, Washington. Journal of Shellfish Research 8:318. Bradbury, A. 1991. Management and stock assessment of the red sea urchin (Strongylocentrotus franciscanus ) in Washington State: Periodic rotation of the fishing grounds. Journal of Shellfish Research [J. SHELLFISH RES.] 10:233 p. Bradbury, A., D. P. Rothaus, R. Sizemore, and M. Ulrich. 2000. A tag method for estimating the natural mortality rate of geoducks (Panopea abrupta). Journal of Shellfish Research 19:690. Brenchley, G. A. 1981. Disturbance and Community Structure: An Experimental Study of Bioturbation in Marine Soft-Bottom Environments. Journal of Marine Research 39:767-790. Brennan, J., and H. Culverwell. 2004. Marine riparian: an assessment of riparian functions in marine ecosystems.in W. S. G. National Oceanic and Atmospheric Administration, editor. Britton-Simmons, K. H. 2004. Direct and indirect effects of the introduced alga Sargassum muticum on benthic, subtidal communities of Washington State, USA. Marine Ecology Progress Series 277:61-78. Britton-Simmons, K. H., J. Eckman, and D. Duggins. 2008. Effect of tidal currents and tidal stage on estimates of bed size in the kelp Nereocystis luetkeana. Marine Ecology Progress Series 355:95-101. Broadhurst, G. 2005. Creosote removal in the Northwest Straits: an important piece of nearshore marine habitat restoration.in Puget Sound Georgia Basin Conference, 2005. Proceedings of the Puget Sound Georgia Basin Research conference. Brock, J. C., M. Palaseanu-Lovejoy, C. W. Wright, and A. Nayegandhi. 2008. Patch-reef morphology as a proxy for Holocene sea-level variability, Northern Florida Keys, USA. Coral Reefs 27:555-568. Broitman, B. R., and B. P. Kinlan. 2006. Spatial scales of benthic and pelagic producer biomass in a coastal upwelling ecosystem. Marine Ecology-Progress Series 327:15-25. Brown, D. W., A. J. Friedman, P. G. Prohaska, and W. D. MacLeod, Jr. 1981. Investigation of Petroleum in the Marine Environs of the Strait of Juan de Fuca and Northern Puget Sound. Part 2: Second-Year Continuation. Report NOAA-TM-OMPA-7.

109 Buck, K. R., and J. Newton. 1995. Fecal pellet flux in Dabob Bay during a diatom bloom: Contribution of microzooplankton. Limnology and Oceanography 40:306-315. Buckley, R. M. 1997. Substrate associated recruitment of juvenile Sebastes in artificial reef and natural habitats in Puget Sound and the San Juan Archipelago, Washington. Page 320 in W. D. o. F. a. Wildlife, editor. Bulthuis, D. A. 1992. Distribution and summer standing crop of seagrasses and macroalgae in Padilla Bay, Washington, 1989. Northwest Science [NORTHWEST SCI.] 66:113 p. Burnett, L. E., and C. S. Milardo. 2000. Inside the shell of an intertidal oyster: Liabilities and benefits? Journal of Shellfish Research 19:642 p. Busby, P. J., T. C. Wainwright, G. J. Bryant, L. J. Lierheimer, R. S. Waples, F. W. Waknitz, and I. V. Lagomarsino. 1996. Status review of west coast steelhead from Washington, Idaho, Oregon and California.in U. D. o. Commerce, editor. Byers, J. E. 2005. Marine reserves enhance abundance but not competitive impacts of a harvested nonindigenous species. Ecology 86:487-500. Byers, J. I. 2002. Physical habitat attribute mediates biotic resistance to non-indigenous species invasion. Oecologia 130:146-156. Caffey, A., B. Blake, and W. Cooke. 2001. Enhancement efforts on state tidelands by the WDFW intertidal shellfish enhancement project. Journal of Shellfish Research 20:1195. Caldeira, K., and M. E. Wickett. 2005. Ocean model predictions of chemistry changes from carbon dioxide emissions to the atmosphere and ocean. Journal of Geophysical Research-Oceans 110:-. Campbell, W. W., and J. A. Cahalan. 1996. WDFW intertidal bivalve population assessment in Puget Sound and Hood Canal, Washington. Journal of Shellfish Research 15:786. Cardwell, R. D., and R. R. Koons. 1981. Biological consideration for the siting and design of marinas and affiliated structures in Puget Sound. Report WDF-TR-60. Carney, D., and R. G. Kvitek. 1990. Shallow subtidal survey of the Washington outer coast and Olympic National Park to determine the distribution, fate, and effects of spilled bunker C fuel oil. Report OCS/MMS- 90/0073. Carney, L. T., J. Waaland, T. Klinger, and K. Ewing. 2005. Restoration of the bull kelp Nereocystis luetkeana in nearshore rocky habitats. Marine Ecology Progress Series 302:49-61. Carr, E. M., and B. R. Dumbauld. 2000. Status of the European green crab invasion in Washington coastal estuaries: Can expansion be prevented? Journal of Shellfish Research 19:629-630. Carr, M. H. 1983. Spatial and temporal patterns of recruitment of young-of-the-year rockfishes (genus Sebastes) into a central California kelp forest. MS thesis. San Francisco State University, San Francisco. Carroll, M. L., and D. S. Wethey. 1990. Predator foraging behavior: Effect of a novel prey species on prey selection by a marine intertidal gastropod. Journal of Experimental Marine Biology and Ecology 139:101-117. Carter, S. K., and G. R. VanBlaricom. 2002. Effects of experimental harvest on red sea urchins (Strongylocentrotus franciscanus) in northern Washington. Fisheries Bulletin 100:662-673. Carter, S. K. C., G. R. VanBlaricom, and B. L. Allen. 2007. Testing the generality of the trophic cascade paradigm for sea otters: a case study with kelp forests in northern Washington, USA . Hydrobiologia 579:233-249. Cheney, D., R. Elston, B. MacDonald, K. Kinnan, and A. Suhrbier. 2001a. Summer mortality of the Pacific oyster Crassostrea gigas: Influences of culture methods, site conditions, and stock selection. World Aquaculture Society, 143 J.M Parker Coliseum Louisiana State University Baton Rouge LA 70803. Cheney, D., R. Elston, B. MacDonald, K. Kinnan, and A. Suhrbier. 2001b. The roles of environmental stressors and culture methods on the summer mortality of the Pacific oyster Crassostrea gigas. Journal of Shellfish Research 20:1195. Cheney, D., R. Oestman, G. Volkhardt, and J. Getz. 1994. Creation of rocky intertidal and shallow subtidal habitats to mitigate for the construction of a large marina in Puget Sound, Washington. Cheney, D. P., R. Elston, and B. MacDonald. 1998. Oyster summer mortality--an update on ongoing sea grant sponsored research. Journal of Shellfish Research [J. Shellfish Res.] 17:no. Chew, K. K. 1988. Littleneck clam aquaculture in the Pacific Northwest. Report; Conf. AK-SG-88-4. Chia, F. S. 1971. Diesel oil spill at Anacortes. Mar. Pollut. Bull 2:105-106. Child, J. I., and W. W. Campbell. 2000. Management of intertidal bivalves in Puget Sound, Washington. Journal of Shellfish Research 19:619-620. Clague, J. J., J. L. Luternauer, and R. J. Hebda. 1983. Sedimentary environments and postglacial history of the Fraser Delta and lower Fraser Valley, British Columbia. Can. J. Earth Sci./J. Can. Sci. Terre 20:1314-1326. Clark, M. P., and K. K. Chew. 1976. Growth of Pacific oysters Crassostrea gigas and related fouling problems under tray culture at Seabeck Bay, Washington. Proc. Natl. Shellfish. Assoc., Med., 66, 34-41, (1976). Clark, R. C., Jr., B. G. Patten, and E. E. DeNike. 1978. Observations of a cold-water intertidal community after 5 years of a low-level, persistent oil spill from the General M.C. Meigs. J. Fish. Res. Board Can. 35:754-765.

110 Clifton, H. E., K. A. Kvenvolden, and J. B. Rapp. 1984. Spilled oil and infaunal activity - modification of burrowing behavior and redistribution of oil. Marine Environmental Research 11:111-136. Coats, D. A., E. Imamura, A. K. Fukuyama, J. R. Skalski, S. Kimura, and J. Steinbeck. 1999. Monitoring of biological recovery of Prince William Sound intertidal sites impacted by the Exxon Valdez oil spill.in N. O. S. National Oceanic and Atmospheric Administration, editor. NOAA Central Library, Silver Spring, MD. Cohen, A, Mills, C., Berry, H., Wonham, M., Bingham, B., Bookheim, B., Carlton, J., Chapman, J., Cordell, J., Harris, L, Klinger, T., Kohn, A., Lambert, C., Lambert, C., Li, K., Secord, D., & Toft, J. (1998). Puget Sound Expedition: A Rapid Assessment Survey of Non-indigenous Species in the Shallow Waters of Puget Sound. Olympia, WA: DNR Nearshore Habitat Program. Cohen, A.N., Berry, H.D., Mills, C.E., Milne, D., Britton-Simmons, K., Wonham, M.J., Secord, D.L., Barkas, J.L., Bingham, B., Bookheim, B.E., Byers, J.E., Chapman, J.W., Cordell, J.R., Dumbauld, B., Fukuyama, A., Harris, L.H., Kohn, A.J., Li, K., Mumford Jr., T.F., Radashevsky, V., Sewell, A.T., & Welch, K. (2001). Washington State Exotics Expedition 2000: A Rapid Survey of Exotic Species in the Shallow Waters of Elliot Bay, Totten and Eld Inlets and Willapa Bay. Olympia, WA: DNR Nearshore Habitat Program. Collier, T. K. 1994. Remediation of contaminated subtidal sediments: How do we proceed? TROMSOE UNIVERSITY, TROMSOE (NORWAY). Congleton, J. L., and J. E. Smith. 1976. Interactions between juvenile salmon and benthic invertebrates in the Skagit salt marsh. [1. Pacific Northwest Technical Workshop of Fish Food Habits Studies; Astoria, OR (USA); 13 Oct 1976]. Report. Connolly, S. 1999. A Latitudinal Gradient in the Structure of Rocky Intertidal Communities: Benthic-oceanic Coupling in the Northeast Pacific Ocean. Dissertation. Cook, A. E. 1996. Intertidal shellfish management on public tidelands in Puget Sound, Washington -- the management process. Journal of Shellfish Research 15:786. Coots, R. 1999. Water quality data compilation and TMDL ranking for the San Juan Islands.in W. S. D. o. Ecology, editor. Copping, A. E., and W. L. Mark. 2004. Training Recreational Divers to Monitor Aquatic Nuisance Species (ANS) in Puget Sound. Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Cox, K., J. Newton, J. Bos, V. Trainer, N. Adams, K. Baugh, D. Cheney, and A. Christy. 2004. On the Origin of Harmful Algal Bloom Species in Pacific Coast Estuaries: Perspectives from the Olympic Region Harmful Algal Bloom (ORHAB) Project. Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Dagg, M. J., B. W. Frost, and J. Newton. 1998. Diel vertical migration and feeding in adult female Calanus pacificus, Metridia lucens and Pseudocalanus newmani during a spring bloom in Dabob Bay, a fjord in Washington USA. Journal of Marine Systems 15:503-509. Damron, E. D., and K. Campbell. 2010. Addendum: Preliminary analytical screening for soil and water, San Juan Island Study, Washington. Earth Solutions NW, LLC. Davis, J. 1998. Intertidal bag culture of Manila clams. Davis, J. P. 1988. Growth rate of sibling diploid and triploid oysters, Crassostrea gigas. Journal of Shellfish Research 7:202. Dawes, C. J. 1998. Marine Botany. John Wiley & Sons, Inc, New York. Dayton, P. 1985. Ecology of Kelp Communities. Ann. Rev. Ecol. Syst. 16:215-245. Dayton, P., and M. Tegner. 1984. Catastrophic storms, El Nino, and patch stability in a southern kelp forest community. Science 224:283-285. Dayton, P. K. 1971. Competition, disturbance, and community organization: the provision and subsequent utilization of space in a rocky intertidal community. Ecol. Monogr 41:351-389. DePhelps, C. 1996. Partnerships for preserving and enhancing the Padilla Bay agriculture/estuarine ecosystem. Journal of Soil and Water Conservation 51:274-279. Dethier, M. N. 1987. The distribution and reproductive phenology of intertidal fleshy crustose algae in Washington. Can. J. Bot./J. Can. Bot 65:1838-1850. Dethier, M. 1990. A Marine and Estuarine Habitat Classification System for Washington State. Report to the Washington Department of Natural Resources, Natural Heritage Program Dethier, M. N. 1991. Effects of an oil spill and freeze event on intertidal community structure in Washington. Report OCS/MMS-91/0002. Dethier, M. N. 1992. Sampling biodiversity of the marine intertidal zone of the Olympic Coast. Northwest Environ. J 8:139-140. Dethier, M. N. 1994. The ecology of intertidal algal crusts: Variation within a functional group. Journal of Experimental Marine Biology and Ecology 177:37-71.

111 Dethier, M.N. 2007. Long-term and seasonal trends of shoreline biota in Puget Sound: analyses of data collected through 2006. Report to the Washington State Dept. of Natural Resources, Nearshore Habitat Program, June 2007. Dethier, M. N., and D. O. Duggins. 1984. An "indirect commensalism" between marine herbivores and the importance of competitive hierarchies. American Naturalist 124:205-219. Dethier, M. N., and D. O. Duggins. 1988. Variation in strong interactions in the intertidal zone along a geographical gradient: A Washington-Alaska comparison. Marine ecology progress series. Oldendorf 50:97-105. Dethier, M. N., E. S. Graham, S. Cohen, and L. M. Tear. 1993. Visual versus random-point percent cover estimations: 'Objective' is not always better. Marine ecology progress series. 96:93-100. Dethier, M., and G. Schoch. 2005. The consequences of scale: Assessing the distribution of benthic populations in a complex estuarine fjord. Estuarine, Coastal and Shelf Science 62:253-270. Dethier, M. N., and G. C. Schoch. 2006. Taxonomic sufficiency in distinguishing natural spatial patterns on an estuarine shoreline. Marine Ecology Progress Series 306:41-49. Dethier, M. N., and R. S. Steneck. 2001. Growth and persistence of diverse intertidal crusts: Survival of the slow in a fast-paced world. Marine Ecology Progress Series 223:89-100. Dethier, M.N. and H.D. Berry. 2008. Decadal changes in shoreline biota in Westcott and Garrison Bays, San Juan County. Report to the Washington State Dept. of Natural Resources, Nearshore Habitat Program, May 2008. DeWreede, R. E. 1978. Phenology of Sargassum muticum (Phaeophyta) in the Strait of Georgia, British Columbia. Syesis, 11, 1-9, (1978). DeWreede, R. E. 1980. The effect of some physical and biological factors on a Sargassum muticum community, and their implication for commercial utilization. Symposium on Useful Algae; Pacific Grove, CA (USA); 6 Mar 1980. Didier, A. J., Jr. 1998. Marine Protected Areas of Washington, Oregon, and California. Report. Dinnel, P., D. Armstrong, K. Larsen, J. Armstrong, and B. Pacunski. 1989. Recruitment of Dungeness crab in Puget Sound from oceanic stocks. Journal of Shellfish Research 8:319. Dinnel, P. A., D. A. Armstrong, and R. O. McMillan. 1993. Evidence for multiple recruitment-cohorts of Puget Sound Dungeness crab, Cancer magister. Marine biology , Heidelberg 115:53-63. Duggins, D. 1987. The effects of kelp forests on nearshore environments: Biomass, detritus, and altered flow. Pages 191-201 in G. V. Blaricom and J. Estes, editors. The community ecology of sea otters. Springer-Verlag, New York. Duggins, D., J. E. Eckmann, C. E. Siddon, and T. Klinger. 2001. Interactive roles of mesograzers and current flow in survival of kelps. Marine Ecology Progress Series 223:143-155. Duggins, D., J Eckman, C Siddon, and T Klinger. 2003. Population, morphometric, and biomechanical studies of three understory kelps along a hydrodynamic gradient. Marine Ecology Progress Series 265: 57-76. Marine Ecology Progress Series 265. Duggins, D. O. 1980. Kelp beds and sea otters: an experimental approach. Ecology 61:447-453. Duggins, D. O. 1981. Sea Urchins and Kelp: The Effects of Short Term Changes in Urchin Diet. Limnology and Oceanography 26:391-394. Duggins, D. O., and M. N. Dethier. 1985. Experimental studies of herbivory and algal competition in a low intertidal habitat. Oecologia 67:183-191. Duggins, D. O., and J. E. Eckman. 1994. The role of kelp detritus in the growth of benthic suspension feeders in an understory kelp forest. Journal of Experimental Marine Biology and Ecology 176:53-68. Duggins, D. O., J. E. Eckman, and A. T. Sewell. 1990. Ecology of understory kelp environments. 2. Effects of kelps on recruitment of benthic invertebrates. Journal of Experimental Marine Biology and Ecology 143:27-45. Duggins, D. O., and J. E. Eckmann. 1997. Is kelp detritus a good food for suspension feeders? Effects of kelp species, age and secondary metabolites. Marine Biology 128:489-495. Duggins, D. O., J. E. Eckmann, C. E. Siddon, and T. Klinger. 2003. Population, morphometric and biomechanical studies of three understory kelps along a hydrodynamics gradient. Marine Ecology Progress Series 265:57- 76. Duggins, D. O., C. A. Simenstad, and J. A. Estes. 1989. Magnification of secondary production by kelp detritus in coastal marine ecosystems. Science (Washington) 245:170-173. Dumbauld, B., D. Armstrong, C. Roegner, K. Feldman, L. Loggerwell, and S. Rumrill. 2001a. Implementing a study to determine the value of molluscan shellfish culture areas as fish habitat in West Coast estuaries. Journal of Shellfish Research 20:1196. Dumbauld, B. R. 2002. The role of oyster aquaculture as habitat in [USA] West Coast estuaries: A review. Puget Sound Action Team, PO Box 40900 Olympia WA 98504.

112 Dumbauld, B. R., D. A. Armstrong, D. R. Gunderson, and A. R. Black. 1988. The importance of intertidal shell as nursery habitat for young-of-the-year Dungeness crab in Grays Harbor, Washington. Journal of Shellfish Research 7:115. Dumbauld, B. R., D. A. Armstrong, and T. L. McDonald. 1993. Use of oyster shell to enhance intertidal habitat and mitigate loss of Dungeness crab (Cancer magister) caused by dredging. Canadian Journal of Fisheries and Aquatic Sciences 50:381-390. Dumbauld, B. R., D. A. Armstrong, and J. Skalski. 1997. Efficacy of the pesticide carbaryl for Thalassinid shrimp control in Washington state oyster (Crassostrea gigas, Thunberg, 1793) aquaculture. Journal of Shellfish Research 16:503-518. Dumbauld, B. R., K. M. Brooks, and M. H. Posey. 2001b. Response of an Estuarine Benthic Community to Application of the Pesticide Carbaryl and Cultivation of Pacific Oysters (Crassostrea gigas) in Willapa Bay, Washington. Marine Pollution Bulletin 42:826-844. Dumbauld, B. R., S. P. Ferraro, and F. A. Cole. 2000a. Oyster aquaculture and benthic invertebrate communities in west coast estuaries: An update. Journal of Shellfish Research 19:608-609. Dumbauld, B. R., and B. E. Kauffman. 1998. The nascent invasion of green crab (Carcinus maenas) in Washington state coastal estuaries. Journal of Shellfish Research [J. Shellfish Res.] 17:no. Dumbauld, B. R., R. E. Kauffman, D. A. Armstrong, E. Visser, and L. Cole-Warner. 1998. Use of oyster shell to create habitat for juvenile dungeness crab in Washington coastal estuaries: Status and prospects. Journal of Shellfish Research [J. Shellfish Res.] 17:no. Dumbauld, B. R., M. Peoples, D. A. Armstrong, and S. G. Ratchford. 1996. A comparison of the effects of three different habitat modifications on intertidal clam populations in Pacific Northwest coastal estuaries. Journal of Shellfish Research 15:480. Dumbauld, B. R., M. Peoples, L. Holomb, J. Tagart, and S. Ratchford. 1995. The potential influence of cordgrass Spartina alterniflora on clam resources in Willapa Bay, Washington. Dumbauld, B. R., E. P. Visser, D. A. Armstrong, L. Cole-Warner, K. L. Feldman, and B. E. Kauffman. 2000b. Use of oyster shell to create habitat for juvenile Dungeness crab in Washington coastal estuaries: Status and prospects. Journal of Shellfish Research 19:379-386. Dumbauld, B. R., and S. Wyllie-Echeverria. 2003. The influence of burrowing thalassinid shrimps on the distribution of intertidal seagrasses in Willapa Bay, Washington, USA. Aquatic Botany 77:27-42. Dunton, K. H., and D. M. Schel. 1987. Dependence of consumers on macroalgal (Laminaria solidungula) carbon in an Arctic kelp community: delta13C evidence. Marine Biology 93:615-625. Eckman, J. E., and D. O. Duggins. 1991. Life and death beneath macrophyte canopies: Effects of understory kelps on growth rates and survival of marine, benthic suspension feeders. Oecologia 87:473-487. Eckman, J. E., D. O. Duggins, and A. T. Sewell. 1989. Ecology of understory kelp environments. 1. Effects of kelps on flow and particle transport near the bottom. Journal of Experimental Marine Biology and Ecology 129:173-187. Eckman, J. E., D. O. Duggins, and C. E. Siddon. 2003. Current and wave dynamics in the shallow subtidal: Implications to the ecology of understory and surface-canopy kelps. Marine Ecology Progress Series 265:45-56. Eggleston, D. B., and D. A. Armstrong. 1995. Pre- and post-settlement determinants of estuarine Dungeness crab recruitment. Ecological Monographs 65:193-216. Eggleston, D. B., D. A. Armstrong, W. E. Elis, and W. S. Patton. 1998. Estuarine fronts as conduits for larval transport: Hydrodynamics and spatial distribution of Dungeness crab postlarvae. Marine Ecology Progress Series 164:73-82. Eilers, H. P., A. Taylor, and W. Sanville. 1982. Vegetative delineation of coastal salt marsh boundaries: Evaluation of methodology. Report EPA-600/3-82-037. Eilers, H. P., A. Taylor, and W. Sanville. 1984. Vegetative delineation of coastal salt marsh boundaries. Report EPA/600/D-84/275. Einav, R., K. Harussi, and D. Perry. 2002. The footprint of the desalination processes on the environment. Desalination 152:141-154. Eisenhardt, E. 2001. Effect of the San Juan Islands Marine Preserves on Demographic Patterns of Nearshore Rocky Reef Fish. MS. University of Washington, Seattle. Eisenhardt, E. 2007. San Juan County Bottomfish Recovery Project: 2006 Biological Assessment Final Report. San Juan Co. Marine Resources Committee, Friday Harbor, WA. Ellifrit, N. J., M. S. Yoshinaka, and D. W. Coon. 1973. Some observations of clam distribution at four sites on Hood Canal, Washington. Proc. Natl. Shellfish. Assoc 63:p. Elzinga, C. L., D. W. Salzer, J. W. Willoughby, and J. P. Gibb. 2001. Monitoring Plant and Animal Populations. Blackwell Science Inc., Malden, MA.

113 Emmett, B., D. Harper, S. Myhill-Jones, M. Morris, and P. Thuringer. 2004. Using Internet-based Mapping to Improve the Accessibility of Intertidal and Backshore Inventory and Ecological Evaluation Information for Victoria and Esquimalt Harbours. Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Emmett, R., R. Lianso, J. Newton, R. Thom, M. Hornberger, C. Morgan, C. Levings, A. Copping, and P. Fishman. 2000. Geographic Signatures of North American West Coast Estuaries. Estuaries 23:765-792. Environmental_Protection_Agency. 1991. Reconnaissance survey of chemical contamination and biological effects in southern Puget Sound. Report EPA/910/9-90/025. Evans, N., and N. West. 1980. Aquaculture siting issues in Washington's coastal zone. Ewing, K. 1983. Environmental controls in Pacific Northwest intertidal marsh plant communities. Can. J. Bot 61:1105-1116. Ewing, K. 1984. Plant growth and productivity along complex gradients in a Pacific northwest brackish intertidal marsh. Estuaries 9:49-62. Fabry, V. J. 1990. Shell growth rates of pteropod and heteropod mollusks and Aragonite production in the open ocean: Implications for the marine carbonate system. Journal of Marine Research 48:209-222. Feely, R. A., and e. al. 2004. The impact of anthropogenic CO2 on the CaCO3 system in the oceans. Science 305. Ferdana, Z. 2002. Marine, nearshore and estuarine conservation targets for the Puget Trough/Georgia Basin ecoregion: Integrating the marine component of an ecoregional plan into a geographic information system (GIS). Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Fernandez, E., O. Iribarne, and D. A. Armstrong. 1994. Habitat selection by young of the year dungeness crab Cancer magister Dana and predation risk in intertidal habitats. Journal of Shellfish Research 13:291-292. Fernandez, M., D. Armstrong, and O. Iribarne. 1993a. First cohort of young-of-the-year Dungeness crab, Cancer magister, reduces abundance of subsequent cohorts in intertidal shell habitat. Canadian Journal of Fisheries and Aquatic Sciences 50:2100-2105. Fernandez, M., O. Iribarne, and D. Armstrong. 1993b. Habitat selection by young-of-the-year Dungeness crab Cancer magister and predation risk in intertidal habitats. Marine ecology progress series. Oldendorf 92:171-177. Ferraro, S. P., and F. A. Cole. 2002. A field validation of two sediment-amphipod toxicity tests. Environmental Toxicology and Chemistry 21:1423-1437. Ferraro, S. P., and F. A. Cole. 2004. Optimal Benthic Macrofaunal Sampling Protocol for Detecting Differences Among Four Habitats in Willapa Bay, Washington, USA. Estuaries 27:1014-1025. Freidenburg, T. L., B. A. Menge, P. M. Halpin, M. Webster, and A. Sutton-Grier. 2007. Cross-scale variation in top- down and bottom-up control of algal abundance. Journal of Experimental Marine Biology and Ecology 347:8-29. Fresh, K. L., T. Wyllie-Echeverria, S. Wyllie-Echeverria, and B. W. Williams. 2006. Using light-permeable grating to mitigate impacts of residential floats on eelgrass Zostera marina L. in Puget Sound, Washington. Ecological Engineering 28:354-362. Friedman, C. S., C. A. Burge, D. P. Cheney, R. A. Elston, A. D. Suhrbier, G. N. Cherr, F. J. Griffin, A. Hamdoun, and C. J. Langdon. 2003. Summer mortality of the Pacific oyster, Crassostrea gigas, along the West Coast of the U.S.: Performance of family lines and environmental parameters. Journal of Shellfish Research 22:603. Friends_of_the_San_Juans. 2004a. Documented surf smelt and Pacific sand lance spawning beaches in San Juan County with a summary of protection and restoration projects for forage fish habitat. Friday Harbor, Washington (unpublished report) Friends_of_the_San_Juans. 2004b. Exploratory Pacific herring spawning habitat surveys for San Juan County, WA. Final report to the Washington State Salmon Recovery Funding Board., Friends of the San Juans, Friday Harbor, Washington. Friends_of_the_San_Juans. 2006. San Juan County Nearshore Impact Assessment (unpublished report) Friends_of_the_San_Juans. 2008. Shoreline Permit Analysis. (unpublished report) Gabrielson, P. W., Widdowson, T. B. & Lindstrom, S. C. 2006. Keys to the seaweeds and seagrasses of Southeast Alaska, British Columbia, Washington and Oregon. University of British Columbia, Department of Botany, Gaeckle, J. L., P. Dowty, B. Reeves, H. Berry, S. Wyllie-Echeverria, and T. Mumford. 2007. Puget Sound Submerged Vegetation Monitoring Project, 2005 Monitoring Report. Washington State Department of Natural Resources, Olympia, WA. Galbraith, H., R. Jones, R. Park, J. Clough, S. Herrod-Julius, B. Harrington, and G. Page. 2002. Global Climate Change and Sea Level Rise: Potential Losses of Intertidal Habitat for Shorebirds. Waterbirds 25:173-183. Gallagher, E. D., P. A. Jumars, and D. D. Trueblood. 1983. Facilitation of soft-bottom benthic succession by tube builders. Ecology 64:1200-1216.

114 Garbary, D. J., K. Y. Kim, T. Klinger, and D. Duggins. 1999. Red algae as hosts for endophytic kelp gametophytes. Marine Biology 135:35-40. Gardiner, W. W., and J. T. Hardy. 1992. Contaminated intertidal surface-film deposits in Puget sound. Garono, R. J., C. A. Simenstad, R. Robinson, and H. Ripley. 2004. Using high spatial resolution hyperspectral imagery to map intertidal habitat structure in Hood Canal, Washington, U.S.A. Canadian Journal of Remote Sensing/Journal Canadien de Teledetection 30:54-63. Gaydos, J. K., K. C. Balcomb III, R. W. Osborne, and L. Dierauf. 2004. Evaluating potential infectious disease threats for southern resident killer whales, (Orcinus orca): A model for endangered species. Biological Conservation 117:253-262. Getter, C. D., and M. O. Hayes. 1981. The comparative sensitivities of five U.S. estuaries to oil and hazardous materials spills. Estuaries 4:244. Ghelardi, R. J. 1971. Species structure of the animal community that lives in Macrocystis pyrifera holdfasts, in: North, W.J. (ed) The biology of giant kelp beds (Macrocystis) in California. Nova Hedwigia 32:381-420. Gillespie, G. E., and N. F. Bourne. 2004. Biology and fisheries of the exotic varnish clam (Nuttallia obscurata) in British Columbia. Journal of Shellfish Research 23:655. Gillespie, G. E., A. R. Kronlund, and G. D. Heritage. 1998. Intertidal clam stock estimates for selected depuration harvest beaches -- 1994. Report 0706-6457, Department of Fisheries and Oceans, Nanaimo, BC [Canada] Sci. Branch. Giver, K. 1999. Effects of the Invasive Seaweed Sargassum muticum on Native Marine Communities in Northern Puget Sound, Washington. Massachusetts Institute of Technology, 292 Main Street, E38-300 Cambridge MA 02139. Godin, G. 1984. A comparison between two simultaneous sets of current measurements in the Strait of Juan de Fuca. Estuarine, Coastal and Shelf Science 19:451-461. Gooding RA, Harley CDG, Tang E (2009) Elevated water temperature and carbon dioxide concentration increase the growth of a keystone echinoderm. Proceedings of the National Academy of Sciences:- Goodwin, C. L., and B. Pease. 1989. Species profiles: Life histories and environmental requirements of coastal fishes and invertebrates (Pacific Northwest). Pacific geoduck clam. Report BIOLOGICAL-82(11.120). Goodwin, L. 1972. Distribution of subtidal hardshell clams in Puget Sound, Washington. Proc. Natl. Shellfish. Assoc 62:4-5. Goodwin, L. 1976. The assessment of subtidal geoduck clam populations by visual and photographic techniques. /[Presented at: National Shellfisheries Association Convention; 1975]. Proc. Natl. Shellfish. Assoc., Md., 65, 7-8, (1976). Goodwin, L. 1977. Study of clam resources and evaluation of harvesting gear. Report, Washington Dep. Fish., Olympia, WA (USA). Goodwin, L. 1978. Study of clam resources and evaluation of harvesting gear. Puget Sound subtidal geoduck survey data. Report, Washington Department of Fisheries, Olympia (USA). Goodwin, L., and W. Shaul. 1978. Study of clam resources and evaluation of harvesting gear. Puget Sound subtidal hardshell clam survey data. Report, Washington Department of Fisheries, Olympia (USA). Goodwynn, L. 1977. The effects of season on visual and photographic assessment of subtidal geoduck clam (Panope generosa Gould) populations. Veliger 20:155-158. Gray, M.A. and C.D. Metcalfe. 1997. Induction of testis-ova in Japanese medaka (Oryzias latipes) exposed to pnonylphenol. Environmental Toxicology and Chemistry 16(5):1082-1086. Green, R. H. 1979. Sampling Design and Statistical Methods for Environmental Biologists. John Wiley and Sons, New York. Grove, R. S., K. Zabloudil, T. Norall, and L. Deysher. 2002. Effects of El Nino events on natural kelp beds and artificial reefs in southern California. ICES Journal of Marine Science 59:S330-S337. Guedelhoefer, C., and B. L. Murdoch. 2000. Changes in the abundance and diversity of intertidal species from 1974- 2000 at Cantilever Pier and Hoffman Cove. University of Washington, Friday Harbor Labs, Friday Harbor, Washington. Guenette, S. 1996. Macrobenthos. Report `1198-6727, Fisheries Centre, University of British Columbia, Vancouver, BC. Gundlach, E. R., P. D. Boehm, M. Marchand, R. M. Atlas, D. M. Ward, and D. A. Wolfe. 1983. The fate of Amoco Cadiz oil. Science (Washington) 221:122-129. Gustafson, R. G., T. C. Wainwright, G. A. Winans, F. W. Waknitz, L. T. Parker, and R. S. Waples. 1997. Status review of sockeye salmon from Washington and Oregon.in U. D. o. Commerce, editor. Gutermuth, F. B., and D. A. Armstrong. 1989. Temperature-dependent metabolic response of juvenile Dungeness crab Cancer magister Dana: Ecological implications for estuarine and coastal populations. Journal of Experimental Marine Biology and Ecology 126:135-144.

115 Hayden-Spear, J. 2006. Nearshore habitat associations of young-of-the-year copper (Sebastes caurinus) and quillback (S. maliger) rockfish in the San Juan Channel, Washington. MS Thesis. University of Washington, Seattle. Hellquist, C., and S. D. Hacker. 2002. Seed production of Spartina anglica, a non-native cordgrass colonizing intertidal habitats of Puget Sound, Washington. Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Helmuth B, Broitman BR, Blanchette CA, Gilman S, Halpin P, Harley CDG, O'Donnell MJ, Hofmann GE, Menge B, Strickland D (2006) Mosaic patterns of thermal stress in the rocky intertidal zone: implications for climate change. Ecol Monogr 76:461-479 Hemminga, M., and C. Duarte. 2000. Seagrass Ecology. Cambridge University Press, New York. Hoelzel, A. R., E. M. Dorsey, and S. J. Stern. 1989. The foraging specializations of individual minke whales. Animal Behavior 38:786-794. Hood_Canal_Dissolved_Oxygen_Program. 2005. Hood Canal Dissolved Oxygen Program. Hodges, B. R., J. E. Furnans, and P. S. Kulis. 2011. Thin-layer gravity current with implications for desalination brine disposal. J. Hydraulic Engineering 137: 356-371. Höpner, T. 1999. A procedure for environmental impact assessments (EIA) for seawater desalination plants. Desalination 124:1-12. Höpner, T., and J. Windelberg. 1996. Elements of environmental impact studies on coastal desalination plants. Desalination 108:11-18. Hughes, Z., and S. Wyllie-Echeverria. 2007. Variation in leaf elongation rates and germination: A pilot study to evaluate the influence of sediment and submarine light on Zostera marina fitness in the San Juan Archipelago. Pages 95-100 Eelgrass Stressor-Response Project, 2005-2007 Report. Washington State Department of Natural Resources, Olympia, Washington. Hurlbert, S. H. 1984. Pseudoreplication and the Design of Ecological Field Experiments. Ecological Monographs 54:187-211. Iglesias-Rodriguez, M. D., P. R. Halloran, R. E. M. Rickaby, I. R. Hall, E. Colmenero-Hidalgo, J. R. Gittins, D. R. H. Green, T. Tyrrell, S. J. Gibbs, P. von Dassow, E. Rehm, E. V. Armbrust, and K. P. Boessenkool. 2008. Phytoplankton calcification in a High-CO2 world. Science 320:336. Iso, S., S. Suizu, and A. Maejima. 1994. The lethal effect of hypertonic solutions and avoidance of marine organisms in relation to discharged brine from a desalination plant. Desalination 97:389-399. Jackson, J. B. C., M. X. Kirby, W. H. Berger, K. A. Bjorndal, L. W. Botsford, B. J. Bourque, R. H. Bradbury, R. Cooke, J. Erlandson, J. A. Estes, T. P. Hughes, S. Kidwell, C. B. Lange, H. S. Lenihan, J. M. Pandolfi, C. H. Peterson, R. S. Steneck, M. J. Tegner, and R. R. Warner. 2001. Historical Overfishing and the Recent Collapse of Coastal Ecosystems. Science 293:629-637. Jeffries, S., H. Huber, J. Calambokidis, and J. Laake. 2003. Trends and status of harbor seals in Washington state: 1978-1999. Journal of Wildlife Management 67:207-218. Johnson, O. W., W. S. Grant, R. G. Kope, K. Neely, F. W. Waknitz, and R. S. Waples. 1997. Status review of chum salmon from Washington, Oregon and California.in U. D. o. Commerce, editor. Johnson, O. W., M. H. Ruckelshaus, W. S. Grant, F. W. Waknitz, A. M. Garrett, G. J. Bryant, K. Neely, and J. J. Hard. 1999. Status review of coastal cutthroat trout from Washington, Oregon and California.in U. D. o. Commerce, editor. Karr, J. R., and E. W. Chu. 1997. Biological monitoring: essential foundation for ecological risk assessment. Human Ecological Risk Assessment 3:993-1004. Kelleher, G., C. Bleakley, and S. Wells. 1995. A global representative system of marine protected areas, vol. 4: South Pacific, Northeast Pacific, Northwest Pacific, Southeast Pacific and Australia/New Zealand. WORLD BANK, WASHINGTON, DC ( ). Kenworthy, W. J., S. Wyllie-Echeverria, R. G. Coles, G. Pergent, and C. Pergent-Martini. 2006. Seagrass Conservation Biology: An Interdisciplinary science for protection of the seagrass biome. Pages 595-623 in A. W. D. Larkum, R. J. Orth, and C. M. Duarte, editors. Seagrass Biology, Ecology and Conservation. Springer, The Netherlands. King County. 2007. Survey of Endocrine Disruptors in King County Surface Waters. Prepared by Richard Jack and Deb Lester, Water and Land Resources Division. Seattle, Washington (unpublished report) Kingsford, M. J. 1998. Analytical Aspects of Sampling Design. Pages 49-83 in M. J. Kingsford and C. N. Battershill, editors. Studying Temperate Marine Environments. A Handbook for Ecologists. Canterbury Univeristy Press, Christchurch, New Zealand.

116 Kingsford, M. J., and C. N. Battershill. 1998. Procedures for Establishing a Study. Pages 29-48 in M. J. Kingsford and C. N. Battershill, editors. Studying Temperate Marine Environments. A Handbook for Ecologists. Canterbury University Press, Christchurch, New Zealand. Kingsford, M. J., C. N. Battershill, and K. Walls. 1998. Introduction to ecological assessments. Pages 17-28 in M. J. Kingsford and C. N. Battershill, editors. Studying Temperate Marine Environments. A Handbook for Ecologists. Canterbury University Press, Christchurch, New Zealand. Klinger, T. 2007. The San Juan County Marine Resources Committee: a case study in cooperative conservation. Frontiers in Ecology and the Environment 5:100-100. Klinger, T., D. K. Padilla, and K. Britton-Simmons. 2006. Two invaders achieve higher densities in reserves. Aquatic Conservation: Marine and Freshwater Ecosystems 16:301-311. Kruzynski, G. M. 2004. Cadmium in oysters and scallops: The BC experience. Toxicology Letters 148:159-169. Kull, K., S. Wyllie-Echeverria, J. Coyle, M. Logsdon, and C. Schietinger. 2007. Differences in water chemistry and light availability within the San Juan Islands. Pages 108-128 Eelgrass Stressor-Response Project, 2005- 2007 Report. Washington State Department of Natural Resources, Olympia, Washington. Lance, M. M., S. A. Richardson, and H. L. Allen. 2004. Washington state recovery plan for the sea otter. Page 91 p. in W. D. o. F. a. Wildlife, editor. Lattemann, S., and T. Höpner. 2008. Environmental impact and impact assessment of seawater desalination. Desalination 220: 1-15. Levings, C. D., J. D. Pringle, and F. Aitkens. 1998. Approaches to Marine Ecosystem Delineation in the Strait of Georgia: Proceedings of a D.F.O. Workshop, Sidney, B.C., 4-5 November 1997. Report; Conference 0706- 6457, Department of Fisheries and Oceans, West Vancouver, BC, Sci. Branch. Long, E., M. Dutch, S. Aasen, K. Welch, and M. Hameedi. 2005. Spatial extent of degraded sediment quality in Puget Sound (Washington State, U.S.A.) based upon measures of the sediment quality triad. Environmental Monitoring and Assessment 111:173-222. Lowenstine, L. J. 2004. Sick Sea Mammals: A Sign of Sick Seas? in 55th Annual Meeting of the American College of Veterinary Pathologists and 39th Annual Meeting of the American Society of Clinical Pathology, Middleton, Wisconsin. MacLeod, W. D., D. W. Brown, R. G. Jenkins, L. S. Ramos, and V. D. Henry. 1976a. A pilot study on the design of a petroleum hydrocarbon baseline investigation for northern Puget Sound and Strait of Juan de Fuca. Report NOAA-TM-ERL-MESA--8, NOAANatl.Analyt.Fac., Environ.Conserv.Div., Seattle, WA, USA. MacLeod, W. D., Jr., D. W. Brown, R. G. Jenkins, and L. S. Ramos. 1976b. Intertidal sediment hydrocarbon levels at two sites on the Strait of Juan de Fuca. Fate and effects of petroleum hydrocarbons in marine ecosystems and organisms, Seattle, WA Malcangio, D., and A. F. Petrillo. 2010. Modeling brine outfall at the planning stage of desalination plants. Desalination 254: 114-125. Mauzey, K. P., C. Birkeland, and P. K. Dayton. 1968. Feeding Behavior of Asteroids and Escape Responses of Their Prey in Puget Sound Region. Ecology 49:603-&. Maxell, B. A., and K. A. Miller. 1996. Demographic Studies of the Annual Kelps Nereocystis luetkeana and Costaria costata (Laminariales, Phaeophyta) in Puget Sound, Washington. Botanica Marina 39:479-489. Mayer, J. R., and N. R. Elkins. 1990. Potential for agricultural pesticide runoff to a Puget Sound estuary: Padilla Bay, Washington. Bulletin of Environmental Contamination and Toxicology 45:215-222. McDonald, P. S., G. C. Jensen, and D. A. Armstrong. 1998. Green crabs and native predators: Possible limitations on the west coast invasion. Journal of Shellfish Research [J. Shellfish Res.] 17:no. McDonald, P. S., G. C. Jensen, and D. A. Armstrong. 2001. The competitive and predatory impacts of the nonindigenous crab Carcinus maenas (L.) on early benthic phase Dungeness crab Cancer magister Dana. Journal of Experimental Marine Biology and Ecology 258:39-54. McDonald, P. S., G. C. Jensen, and D. A. Armstrong. 2003. Biotic resistance to European green crab, Carcinus maenas, by native analogs in the northeastern Pacific. Journal of Shellfish Research 22:606. McDonald, P. S., G. C. Jensen, and D. A. Armstrong. 2004. Between a rock and a hard place: the ecology of ovigerous green crab, Carcinus maenas (L.), with emphasis on implications for monitoring and control efforts. Journal of Shellfish Research 23:657. McGraw, K. A., D. A. Armstrong, F. C. Weinmann, and W. H. Pearson. 1991. An overview of crab mitigation in Grays Harbor, Washington. Journal of Shellfish Research [J. SHELLFISH RES.] 10:305 p. McMillan, R. O., D. A. Armstrong, and P. A. Dinnel. 1988a. Intertidal distribution and abundance of young-of-the- year Dungeness crab Cancer magister in northern inland waters of Washington. Journal of Shellfish Research 7:126-127. McMillan, R. O., D. A. Armstrong, and P. A. Dinnel. 1995. Comparison of intertidal habitat use and growth rates of two northern Puget Sound cohorts of 0+ age Dungeness crab, Cancer magister. Estuaries 18:390-398.

117 McMillan, R. O., P. A. Dinnel, D. A. Armstrong, T. C. Wainwright, and A. J. Whiley. 1988b. Habitat preference of Dungeness crab, Cancer magister, in Padilla Bay, Washington. Journal of Shellfish Research 7:169. Meneses, M., J. C. Pasqualino, R. Céspedes-Sánchez, and F. Castells. 2010. Alternatives for reducing the environmental impact from the main residue from a desalination plant. J. Industrial Ecology 14: 512-527. Menge, B. A. 1972a. Competition for food between two intertidal starfish species and its effect on body size and feeding. Ecology 53:635-644. Menge, B. A. 1972b. Foraging strategy of a starfish in relation to actual prey availability and environmental predictability. Ecol. Monogr 42:25-50. Menge, B. A., G. Allison, T. Freidenburg, M. Kavanaugh, J. Lubchenco, K. J. Nielsen, C. Schock, and S. Wood. 2003. Local to coastal-scale macrophyte community structure: Surprising patterns and possible mechanisms. Journal of Phycology 39:42. Menge, B. A., E. L. Berlow, C. A. Balchette, S. A. Navarrete, and S. B. Yamada. 1994. The keystone species concept: Variation in interaction strength in a rocky intertidal habitat. Ecological Monographs 64:249-286. Mickett, J. B., M. C. Gregg, and H. E. Seim. 2004. Direct measurements of diapycnal mixing in a fjord reach -- Puget Sound's Main Basin. Estuarine, Coastal and Shelf Science 59:539-558. Mills, C. E. 1993. Natural mortality in NE Pacific coastal hydromedusae: Grazing predation, wound healing and senescence. Mills, C. E. 1995. Medusae, siphonophores, and ctenophores as planktivorous predators in changing global ecosystems. ACADEMIC PRESS, LONDON (UK). Mills, C. E. 2001. Jellyfish blooms: are populations increasing globally in response to changing ocean conditions? Hydrobiologia 451:55-68. Mills, C. E. 2002. Ongoing invasion of the Asian purple varnish clam, Nuttallia obscurata, into Puget Sound waters: Does anyone care? Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Mills, C. E., A.N. Cohen, H.K. Berry, M.J. Wonham, B. Bingham, B. Bookheim, J.T. Carlton, J.W. Chapman, J. Cordell, L.H. Harris, T. Klinger, A.J. Kohn, C. Lambert, G. Lambert, K. Li, D.L. Secord, and J. Toft. 2000. The 1998 Puget Sound Expedition: a shallow water rapid assessment survey for nonindigenous species, with comparisons to San Francisco Bay. Proceedings of the National Conference on Marine Bioinvasions, Cambridge, Massachusetts. Mills, L. J., and C. Chichester. 2005. Review of evidence: Are endocrine-disrupting chemicals in the aquatic environment impacting fish populations?. Science of the Total Environment 343: 1-34. Mitchell, T., and R. L. Ford. 2004. Coastal Biota Survey of the Swinomish Tribal Community. Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Mofjeld, H. O. 1992. Subtidal sea level fluctuations in a large fjord system. Journal of Geophysical Research. C. Oceans 97:20191-20199. Moran, A. L. 1999. Size and Performance of Juvenile Marine Invertebrates: Potential Contrasts Between Intertidal and Subtidal Benthic Habitats. American Zoologist 39:304-312. Moulton, L., and D. Penttila. 2001. Field Manual for Sampling Forage Fish Spawn in Intertidal Shore Regions.in M. R. a. W. D. o. F. a. Wildlife, editor. Mumford, T., F. Goetz, H. Shipman, J. Newton, R. Shuman, J. Brennan, C. A. Simenstad, K. Fresh, M. Dethier, M. Logsdon, C. Tanner, D. Myers, and G. Gelfenbaum. 2004. Puget Sound Nearshore Ecosystem Restoration Program: Program Overview, Puget Sound Conceptual Model and Guiding Principles. Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Muñiz-Salazar, R., S. L. Talbot, G. K. Sage, D. H. Ward, and A. Cabello-Pasini. 2006. Genetic structure of eelgrass Zostera marina meadows in an embayment with restricted water ﬂow. Marine Ecology- Progress Series 309:803-812. Murphy, M. L., S. W. Johnson, and D. J. Csepp. 2000. A comparison of fish assemblages in eelgrass and adjacent subtidal habitats near Craig, Alaska. Alaska Fishery Research Bulletin 7:11-21. Murray, S. N., R. F. Ambrose, and M. N. Dethier. 2006. Monitoring Rocky Shores. University of California Press, Berkeley. Myers, J. M., R. G. Kope, G. J. Bryant, D. J. Teel, L. J. Lierheimer, T. C. Wainwright, W. S. Grant, F. W. Waknitz, K. Neely, S. Lindley, and R. S. Waples. 1998. Status review of chinook salmon from Washington, Idaho, Oregon and California.in U. D. o. Commerce, editor. Nearshore_Habitat_Program. 2001. The Washington State Shore Zone Inventory.in W. D. o. N. Resources, editor. Neckles, H. 1994. Indicator development: Seagrass Monitoring and research in the Gulf of Mexico, U.S.in U. S. E. P. Agency, editor. Nelson, T. A. 1997. Interannual variance in a subtidal eelgrass community. Aquatic Botany 56:245-252.

118 Nelson, T. A. 2000. Preliminary studies of seasonality, ecology, and species composition of ulvoid algal blooms in Washington state. Journal of Phycology 36:suppl., 51 p. Nelson, T. A. 2001. Species composition and controls of ulvoid algal blooms in Washington State. Journal of Phycology 37:38-39. Nelson, T. A., and A. Lee. 2001. A manipulative experiment demonstrates that blooms of the macroalga Ulvaria obscura can reduce eelgrass shoot density. Aquatic Botany 71:149-154. Nelson, T. A., A. V. Nelson, and M. Tjoelker. 2003. Seasonal and Spatial Patterns of "Green Tides" (Ulvoid Algal Blooms) and Related Water Quality Parameters in the Coastal Waters of Washington State, USA. Botanica Marina 46:263-275. Nelson, T. A., and J. R. Waaland. 1997. Seasonality of eelgrass, epiphyte, and grazer biomass and productivity in subtidal eelgrass meadows subjected to moderate tidal amplitude. Aquatic Botany 56:51-74. Newton, J. 2003. Climate variability and phytoplankton production in PNW [Pacific Northwest] coast estuaries. Journal of Phycology 39:44. Newton, J., S. Albertson, K. Van Voorhis, C. Maloy, and E. Siegel. 2002. Washington State Marine Water Quality, 1998 through 2000.in W. D. o. Ecology, editor. Newton, J. A., and R. A. Horner. 2003. Use of Phytoplankton Species Indicators to Track the Origin of Phytoplankton Blooms in Willapa Bay, Washington. Estuaries 26:1071-1078. Nichols, F. H. 1972. Benthic polychaete assemblages and their relationship to the sediment in Port Madison, Washington. W.B. Saunders Company, London (England) Nicholson, N. 1971. Sargassum muticum: A Japanese seaweed continues moving into new waters. University press, California. Niemela, J., and H. Tyle. 1989. Risk Assessment: 4-chloro-2-methylphenol. Danish Environmental Protection Agency, Copenhagen, Denmark. NOAA, 2010. Orca Recovery Plan, TBA Norris, J. G., S. Wyllie-Echeverria, T. Mumford, A. Bailey, and T. Turner. 1997. Estimating basal area coverage of subtidal seagrass beds using underwater videography. Aquatic Botany 58:269-287. Nyblade, C. F. 1979. The intertidal and shallow subtidal benthos of the Strait of Juan de Fuca spring 1976 - winter 1977. Report, U.S. Environmental Research Laboratories, Boulder, CO. Marine Ecosystems Analysis Program. Nysewander, D. R., J. R. Evenson, B. L. Murphie, and T. A. Cyra. 2002. Report of Marine Bird and Marine Mammal Component, Puget Sound Ambient Monitoring Program, for July 1992 to December 1999 Period.in W. D. o. F. a. Wildlife, editor. O'Donnell MJ, Hammond L, Hofmann GE (2009) Predicted impact of ocean acidification on a marine invertebrate: elevated CO2 alters response to thermal stress in sea urchin larvae. Mar Biol 156:439-446 Olson, A. 2008. Shifting Baselines in the Sound: Video Presentation. in P. S. Partnership, editor. Orr, J. C., V. J. Fabry, O. Aumont, L. Bopp, S. C. Doney, R. A. Feely, A. Gnanadesikan, N. Gruber, A. Ishida, F. Joos, R. M. Key, K. Lindsay, E. Maier-Reimer, R. Matear, P. Monfray, A. Mouchet, R. G. Najjar, G. Plattner, K. B. Rodgers, C. L. Sabine, J. L. Sarmiento, R. Schlitzer, R. D. Slater, I. J. Totterdell, M. Weirig, Y. Yamanaka, and A. Yool. 2005. Anthropogenic ocean acidification over the twenty-first century and its impact on calcifying organisms. Nature 437:681-686. Osenberg, C. W., and R. J. Schmitt. 1996. Detecting Ecological Impacts Caused by Human Activities. Pages 3-16 in R. J. Schmitt and C. W. Osenberg, editors. Detecting Ecological Impacts Concepts and Applications in Coastal Habitats. Academic Press, New York. Osenberg, C. W., R. J. Schmitt, S. J. Holbrook, K. Abu-Saba, and A. R. Flegal. 1996. Detection of Environmental Impacts: Natural Variation, Effect Size and Power Analysis. Pages 83-107 in R. J. Schmitt and C. W. Osenberg, editors. Detecting Ecological Impacts Concepts and Applications in Coastal Habitats. Academic Press, New York. Paine, R. T. 1974. intertidal community structure. Experimental studies on the relationship between a dominant competitor and its principal predator. Oecologia 15:93-12O. Paine, R. T. 1976. Size-limited predation: an observational and experimental approach with the Mytilus-Pisaster interaction. Ecology 57:858-873. Paine, R. T. 1986. Benthic community-water column coupling during the 1982-1983 El Nino. Are community changes at high latitudes attributable to cause or coincidence? Limnology and Oceanography 31:351-360. Paine, R. T. 1992. Studies on processes influencing biological diversity on rocky shores. Northwest Environ. J 8:148-150. Paine, R. T. 2002. Trophic Control of Production in a Rocky Intertidal Community. Science (Washington) 296:736- 739.

119 Paine, R. T., and S. A. Levin. 1981. Intertidal Landscapes: Disturbance and the Dynamics of Pattern. Ecological Monographs 51:145-178. Paine, R. T., J. L. Ruesink, A. Sun, E. L. Soulanilee, M. J. Wonham, C. D. G. Harley, D. R. Brumbaugh, and D. L. Secord. 1996. Trouble on oiled waters: lessons from the Exxon Valdez oil spill. Annual Review of Ecology and Systematics 27:197-235. Paine, R. T., and A. C. Trimble. 2004. Abrupt community change on a rocky shore - biological mechanisms contributing to the potential formation of an alternative state. Ecology Letters 7:441-445. Palacios, R., and D. A. Armstrong. 1989. Predation of juvenile soft shell-clam (Mya arenaria ) by juvenile Dungeness crab (Cancer magister). Journal of Shellfish Research 8:445-446. Palacios, R., D. A. Armstrong, and J. Orensanz. 2000. Fate and legacy of an invasion: extinct and extant populations of the soft-shell clam (Mya arenaria) in Grays Harbor (Washington). Aquatic Conservation: Marine and Freshwater Ecosystems 10:279-303. Palomar, P., and I. J. Losada. 2010. Desalination in Spain: Recent developments and recommendations. Desalination 255: 97-106. Palsson, W. A., J. C. Hoeman, G. G. Bargmann, and D. E. Day. 1997. 1995 status of Puget Sound bottomfish stocks (revised). Page 98 p. in W. D. o. F. a. Wildlife, editor. Parrish, J. D., D. P. Bruan, and R. S. Unnasch. 2003. Are we conserving what we say we are? Measuring ecological integrity within protected areas. BioScience 53:851-860. Pease, B., and K. Cooper. 1988. A relationship between selective larval settlement and adult distribution patterns of geoduck clams and the presence of chaetopterid polychaete tube mats in Puget Sound, Washington. Journal of Shellfish Research 7:129. Penttila, D. E. 1997. Investigations of intertidal spawning habitats of surf smelt and Pacific sand lance in Puget Sound, Washington. American Fisheries Society. Penttila, D. 1999. Documented spawning areas of the Pacific herring (Clupea), surf smelt (Hypomesus), and Pacific sand lance (Ammodytes) in San Juan County, Washington. Washington Department of Fish and Wildlife, Marine Resources Division. Penttila, D. E. 2001. Intertidal spawning ecology of three species of marine forage fishes in Washington State. Journal of Shellfish Research 20:1198. Peterson, C. H., S. D. Rice, J. W. E. Short, D., J. L. Bodkin, B. E. Ballachey, and D. B. Irons. 2003. Long-term ecosystem response to the Exxon Valdez oil spill. Science 302:2082-2086. Pfister, C. A. 1992. Sculpin diversity in tidepools. Northwest Environ. J 8:156-157. Phillips, R. 1984. The ecology of eelgrass meadows in the Pacific Northwest: A community profile.in U. S. F. a. W. Service, editor. Poiani, K. A., J. V. Baumgartner, S. C. Buttrick, S. L. Green, E. Hopkins, G. D. Ivey, K. P. Seaton, and R. D. Sutter. 1998. A scale-independent, site conservation planning framework in The Nature Conservancy. Landscape and Urban Planning 43:143-156. Poiani, K. A., B. D. Richter, M. G. Anderson, and H. E. Richter. 2000. Biodiversity conservation at multiple scales: functional sites, landscapes, and networks. BioScience 50:133-146. Puget_Sound_Action_Team. 2007. 2007 Puget Sound Update: Ninth Report of the Puget Sound Ambient Monitoring Program. Olympia, WA. Puget Sound Partnership. 2011. Science Update. pugetsoundscienceupdate.com accessed on June 27 2011. Puget Sound Partnership. Tacoma, Washington. Puget Sound Shared Strategy, 2005. San Juan County Salmon Recovery Chapter. Quinn, T. 1999. Habitat Characteristics of an Intertidal Aggregation of Pacific Sandlance (at a North Puget Sound Beach in Washington. Northwest Science 73:no. Raventos, N., E. Macpherson, and A. García-Rubiés. 2006. Effect of brine discharge from a desalination plant on macrobenthic communities in the NW Mediterranean. Mar. Environ. Research 62:1-14. Rearick, J., S. Talbot, S. Wyllie-Echeverria, and P. Dowty. 2007. Genetic structure and diversity of Zostera marina in the San Juan Archipelago and Hood Canal, Puget Sound, Washington. Pages 129-197 Eelgrass Stressor- Response Project, 2005-2007 Report. Washington State Department of Natural Resources, Olympia, Washington. Reeder, T. G., and S. D. Hacker. 2004. Factors Contributing to the Removal of a Marine Grass Invader (Spartina anglica) and Subsequent Potential for Habitat Restoration. Estuaries 27:244-252. Reichert, J. 2005. Oil and fuel transfer over waters of the State of Washington: a report to the legislature.in S. P. Washington State Department of Ecology, Preparedness and Response Program, editor. Reise, K. 1985. Predator control in marine tidal sediments. Pages 311-321 in 19th European Marine Biology Symposium, Plymoth, U. K.

120 Rice, C. A. 2007. Evaluating the Biological Condition of Puget Sound. Dissertation for PhD program. University of Washington, Seattle, WA. Rice, C. A., and K. L. Sobocinski. 2004. Effects Of Shoreline Modification on Spawning Habitat of Surf Smelt (Hypomesus pretiosus) in Puget Sound, Washington. Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Richardson, S., D. S. Hays, R., and J. Stofel. 2000. Washington state status report for the common loon. Page 53 p. in W. D. o. F. a. Wildlife, editor. Richardson, S. D. 2008. Environmental mass spectrometry: emerging contaminants and current issues. Anal. Chem. 80: 4373-4402. Rines, J. E. B., P. L. Donaghay, M. M. Dekshenieks, and J. M. Sullivan. 2002. Thin layers and camouflage: hidden Pseudo-nitzschia populations in a fjord in the San Juan Islands, Washngton, USA. Marine Ecology Progress Series 225:123-137. Rodgers, S. A., and B. L. Bingham. 1996. Subtidal zonation of the holothurian Cucumaria lubrica (Clark). Journal of Experimental Marine Biology and Ecology 204:113-129. Rothaus, D. P., R. E. Sizemore, M. J. Ulrich, and C. S. Friedman. 2003. Trends in pinto abalone (Haliotis kamtschatkana) abundance at ten sites in the San Juan Islands and management of the species in Washington State. Journal of Shellfish Research 22:607. Ruckelshaus, M. H. 1995. Estimates of outcrossing rates and of inbreeding depression in a population of the marine angiosperm Zostera marina. Marine biology , Heidelberg 123:583-593. Ruckelshaus, M. H., R. C. Wissmar, and C. A. Simenstad. 1993. The importance of autotroph distribution to mussel growth in a well-mixed, temperate estuary. Estuaries 16:898-912. Ruckelshaus, W. D. 2002. A strategy for recovering salmon in Puget Sound. Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Ruef, W., A. Devol, S. Emerson, J. Dunne, J. Newton, R. Reynolds, and J. Lynton. 2004. In situ and Remote Monitoring of Water Quality in South Puget Sound: The ORCA Time-Series. Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Ruesink, J. L. 1998. Physical and biological impacts on growth and mortality of Crassostrea gigas. Journal of Shellfish Research [J. Shellfish Res.] 17:no. Ruesink, J. L. 2007. Biotic resistance and facilitation of a non-native oyster on rocky shores. Marine Ecology- Progress Series 331:1-9. Ruesink, J. L., G. Curtis Roegner, B. R. Dumbauld, J. A. Newton, and D. A. Armstrong. 2003. Contributions of Coastal and Watershed Energy Sources to Secondary Production in a Northeastern Pacific Estuary. Estuaries 26:1079-1093. Sabine, C. L., and e. al. 2004. The ocean sink for anthropogenic CO2. Science 305:367-370. San Juan County, 2008. SJC Habitat Conservation Plan 2008-2014, SJC Land Bank San Juan County Watershed Management Action Plan & Characterization Report, Final approved August 24, 2000, SJC Health & Community Services San Juan County, December 2008, Interim Aquifer Protection Report, Eastsound, Pacific Groundwater Group San Juan County Marine Resources Committee, Marine Stewardship Area Monitoring Plan, DRAFT, December 15, 2009, San_Juan_Initiative. 2008. http://www.sanjuaninitiative.org/documents.html (unpublished reports) Schanz, A., Julich, H., Ferrier, L., Berry, H., 2010. Eelgrass Stressor-Response Project Report 2007-2008. Zostera marina L. (eelgrass) transplant growth and survival along a tidal gradient in Westcott Bay. Olympia, WA: DNR Nearshore Habitat Program Schmidt, R. V., M. C. Healey, F. P. Jordan, and R. M. Hungar. 1978a. Data record: juvenile salmon and other fish species captured by 50-fathom purse seines in nearshore areas near Nanaimo, 1975. Report, Fisheries and Marine Service, Nanaimo, B.C. (Canada). Pacific Biological Station. Schmidt, R. V., M. C. Healey, F. P. Jordan, and R. M. Hungar. 1978b. Data record: Juvenile salmon and other fish species captured in intertidal areas near Nanaimo, 1975-1976. Report, Fisheries and Marine Service, Nanaimo, B.C. (Canada). Pacific Biological Station. Schmidt, R. V., M. C. Healey, F. P. Jordan, and R. M. Hungar. 1979a. Data record: juvenile salmon and other fish species captured by 50-fathom purse seines in nearshore areas near Nanaimo, 1976. Schmidt, R. V., M. C. Healey, F. P. Jordan, and R. M. Hungar. 1979b. Data record: juvenile salmon and other fish species captured by 120-fathom purse seines in nearshore areas near Nanaimo, 1976-77. Schmidt, R. V., M. C. Healey, F. P. Jordon, and R. M. Hungar. 1978c. Data record: juvenile salmon and other fish species captured by 120-fathom purse seines in nearshore areas near Nanaimo, 1975. Report, Fisheries and Marine Service, Nanaimo, B.C. (Canada). Pacific Biological Station.

121 Schoch, G. C. 2000. Untangling the complexity of nearshore ecosystems: Examining issues of scaling and variability in benthic communities. Dissertation Abstracts International Part B: Science and Engineering 60:4453. Schoch, G. C., and M. N. Dethier. 1996. Scaling up: The statistical linkage between organismal abundance and geomorphology on rocky intertidal shorelines. Journal of Experimental Marine Biology and Ecology 201:37-72. Scholz, A. J., W. A. Cooke, K. L. Cooper, and J. Donaldson. 1985. Beach setting of eyed oyster larvae Crassostrea gigas (Thunberg) in Puget Sound, Washington. Journal of Shellfish Research 5:53. Sebens, K. P. 1981. Reproductive Ecology of the Intertidal Sea Anemones Anthopleura xanthogrammica (Brandt) and A. elegantissima (Brandt): Body Size, Habitat, and Sexual Reproduction. Journal of Experimental Marine Biology and Ecology 54:225-250. Sebens, K. P. 1982. Recruitment and habitat selection in the intertidal sea anemones, Anthopleura elegantissima (Brandt) and A. xanthogrammica (Brandt). Journal of Experimental Marine Biology and Ecology 59:103- 124. Sebens, K. P. 1983. Population dynamics and habitat suitability of the intertidal sea anemones Anthopleura elegantissima and A. xanthogrammica. Ecological Monographs 53:405-433. Sebens, K. P. 1986. Spatial Relationships among Encrusting Marine Organisms in the New-England Subtidal Zone. Ecological Monographs 56:73-96. Sebens, K. P. 1990. Habitat structure and community dynamics in marine benthic systems. Pages 211-234 in E. D. McCoy, S. A. Bell, and H. Mushinsky, editors. Habitat Structure: the Physical Arrangement of Objects in Space. Chapman and Hall, London. Sebens, K. P., and J. R. Lewis. 1985. Rare events and population structure of the barnacle Semibalanus cariosus (Pallas, 1788). Journal of Experimental Marine Biology and Ecology 87:55-65. Secord, D. 2003. Biological Control of Marine Invasive Species: Cautionary Tales and Land-Based Lessons. Biological Invasions 5:117-131. Secord, D. 2004. Deprogramming invasion biologists? A review of David I. Theodoropoulos's Invasion Biology: Critique of a Pseudoscience. Ecology 85:1172-1173. Secord, D., and K. Hemmelgarn. 2004. A field guide to non-native aquatic species of the Pacific Northwest. Tacoma, WA. Seed, R. 2000. Mussels: Space monopolisers or ecosystem-engineers? Journal of Shellfish Research 19:611-612. Seiders, K., C. Deligeannis, and P. Sandvik. 2007. Contaminants in Fish Tissue from Freshwater Environments in 2004 and 2005. Page 35pp in W. D. o. Ecology, editor. Serdar, D., D. Norton, and D. Davis. 2001. Concentrations of selected chemicals in sediments from harbors in the San Juan Islands. in E. A. P. Washington State Department of Ecology, editor. Shaffer, J. A., and D. S. Parks. 1994. Seasonal variations in and observations of landslide impacts on the algal composition of a Puget Sound nearshore kelp forest. Botanica Marina 37:315-323. Shannon, J., and W. Taylor. 2004. Monitoring Puget Sound Forage Fish Habitat: Lessons from the Redondo Seawall Mitigation and Monitoring Project. Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Shen, G. T. 1995. Panel Findings and Recommendations Based on the First Comprehensive Review of the Puget Sound Ambient Monitoring Program . Puget Sound Water Quality Authority, Olympia WA. Shull, S., and D. A. Bulthuis. 2001. Accessible methodology for monitoring estuarine and coastal vegetation cover. U.S. National Oceanic and Atmospheric Administration, NOAA Coastal Services Center 2234 South Hobson Avenue Charleston SC 29405. Sibert, J. R., and V. J. Harpham. 1979. Effects of intertidal log storage on the meiofauna and interstitial environment of the Nanaimo River delta. Report, Fisheries and Marine Service, Nanaimo, BC (Canada). Pacific Biological Station. Simenstad, C. A. 2000. Commencement Bay Aquatic Ecosystem Assessment: Ecosystem-Scale Restoration for Juvenile Salmon Recovery. Technical Report. School of Aquatic and Fishery Science, Fisheries Research Institute, Washington University [Rep. Fish. Res. Inst. Wash. Univ.]:[np]. Simenstad, C. A., D. O. Duggins, and P. D. Quay. 1993. High turnover of inorganic carbon in kelp habitats as a cause of delta super(13)C variability in marine food webs. Marine biology , Heidelberg 116:147-160. Simenstad, C. A., and K. L. Fresh. 1995. Influence of intertidal aquaculture on benthic communities in Pacific Northwest estuaries: Scales of disturbance. Estuaries 18:43-70. Simenstad, C. A., K. L. Fresh, and E. O. Salo. 1981. The role of Puget Sound and Washington coastal estuaries in the life history of Pacific salmon: An unappreciated function. Estuaries 4:285-286. Simenstad, C. A., W. J. Kinney, and B. S. Miller. 1980. Epibenthic zooplankton assemblages at selected sites along the Strait of Juan de Fuca. Report, NOAA Environmental Research Lab., Boulder, CO (USA). Marine Ecosystems Analysis Program.

122 Simenstad, C. A., and E. O. Salo. 1982. Foraging success as a determinant of estuarine and nearshore carrying capacity of juvenile chum salmon (Oncorhynchus keta ) in Hood Canal, Washington. Report; Conference ASG-82-2. Simenstad, C. A., A. Wick, S. Van de Wetering, and D. L. Bottom. 2003. Dynamics and Ecological Functions of Wood in Estuarine and Coastal Marine Ecosystems. American Fisheries Society, 5410 Grosvenor Ln. Ste. 110 Bethesda MD 20814-2199 , [URL http //afs.allenpress.com]. Sizemore, B. 2000. Management of geoduck clams (Panopea abrupta) in Washington State. Journal of Shellfish Research 19:625. Skalski, J. R., D. A. Coats, and A. K. Fukuyama. 2001. Criteria for oil spill recovery: a case study of the intertidal community of Prince William Sound, Alaska, following the Exxon Valdez oil spill. Environmental Management 28:9-18. Skidmore, D., and K. K. Chew. 1985. Mussel aquaculture in Puget Sound. Report WSG-85-4. Skidmore, D. A., K. W. Johnson, and G. W. Raven. 1985. Intertidal, longline culture of Mytilus edulis Linne in Puget Sound, Washington. Journal of Shellfish Research 5:54. Smiley, B., and B. Burd. 2004. Reefkeepers' Monitoring of Artificial Reefs: An Example of Local Citizen Science Involving Recreational Divers and Others on Southeast Vancouver Island. Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Smith, A. L. 1981. Comparison of Macrofaunal Invertebrates in Sand Dollar (Dendraster excentricus ) Beds and in Adjacent Areas Free of Sand Dollars. Marine Biology , Heidelberg 65:191-198. Smith, B. D., E. L. Cabot, and R. E. Foreman. 1985. Seaweed detritus versus benthic diatoms as important food resources for two dominant subtidal gastropods. Journal of Experimental Marine Biology and Ecology 92:143-156. Smith, J. E. 1976. Sampling intertidal salt marsh macrobenthos. [1. Pacific Northwest Technical Workshop of Fish Food Habits Studies; Astoria, OR (USA); 13 Oct 1976]. Report. Speich, S., and T. Wahl. 1989. Catalog of Washington seabird colonies. Page 510 p. in U. S. F. a. W. Service, editor. Speidel, M., C. D. G. Harley, and M. J. Wonham. 2001. Recovery of the brown alga Fucus gardneri following a range of removal intensities. Aquatic Botany 71:273-280. Spencer 2006 algae class at UW FHL (TBA) Stanley, C. A., and B. C. Gregg. 2004. Using GIS to enhance understanding of spatial and temporal intertidal clam distribution patterns in North Puget Sound. Journal of Shellfish Research 23:659. Sterritt, D. A., E. A. Wood, and J. L. Whitney. 1996. Intertidal shellfish harvest assessment in Puget Sound, Washington. Journal of Shellfish Research 15:789. Stevens, B. G., D. A. Armstrong, and J. C. Hoeman. 1984. Diel activity of an estuarine population of Dungeness crabs, Cancer magister, in relation to feeding and environmental factors. Journal of crustacean biology. Washington DC 4:390-403. Stevens, B. G., R. Cusimano, and D. A. Armstrong. 1982. Feeding habits of the Dungeness crab Cancer magister Dana in Grays Harbor, Washington. Journal of Shellfish Research 2:121. Stiller, J. W., and A. L. Denton. 1995. One hundred years of Spartina alterniflora (Poaceae) in Willapa Bay, Washington: Random amplified polymorphic DNA analysis of an invasive population. Molecular Ecology 4:355-363. Stillwater. 2010. DRAFT San Juan County pilot stormwater monitoring plan. Stillwater Sciences, Seattle, Washington (unpublished report) Strand, J. A., V. I. Cullinan, E. A. Crecelius, T. J. Fortman, and R. J. Citterman. 1990. Monitoring of Olympic National Park Beaches to determine fate and effects of spilled bunker C fuel oil. Final report. Report OCS/MMS-90-0061. Strand, J. A., V. I. Cullinan, E. A. Crecelius, T. J. Fortman, R. J. Citterman, and M. L. Fleischmann. 1992. Fate of bunker C fuel oil in Washington coastal habitats following the December 1988 Nestucca oil spill. Northwest Science 66:1-14. Straus, K. M., K. A. Naish, J. P. Davis, and C. S. Friedman. 2005. Restoration of the Pinto abalone (Haliotis kamschatkana): Captive rearing and phylogeography. Journal of Shellfish Research 24:678. Suchanek, T. H. 1981. The Role of Disturbance in the Evolution of Life History Strategies in the Intertidal Mussels Mytilus edulis and Mytilus californianus. Oecologia 50:143-151. Suryan, R. M., and J. T. Harvey. 1998. Tracking harbor seals (Phoca vitulina richardsi) to determine dive behavior, foraging activity, and haul-out site use. Marine Mammal Science 14:361-372. Suttles, W. P. 1951. Economic Life of the Coast Salish of Haro and Rosario Straits. University of Washington, Seattle, WA.

123 Takesue, R. K., E. E. Grossman, S. Wyllie-Echeverria, and J. K. Elliott. 2006. High cadmium may contribute to eelgrass (Zostera marina) habitat loss in Westcott Bay, San Juan Island. Advancing the Science of Limnology & Oceanography (ASLO), Summer Meeting, June 4-9, Victoria, B.C. Tanner, C. D., J. R. Cordell, J. Rubey, and L. M. Tear. 2002. Restoration of Freshwater Intertidal Habitat Functions at Spencer Island, Everett, Washington. Restoration Ecology 10:564-576. Tatarazako, N., K. Yamamoto, and K. Iwasaki. 2002. Subacute toxicity of wood preservatives, DDAC and BAAC, in several aquatic organisms. J. Health Sci. 48(4): 359-365. Thom, R. M. 1980. Seasonality in low intertidal benthic marine algal communities in Central Puget Sound, Washington, USA. Bot. Mar. 23:7-11. Thom, R. M. 1983. Spatial and temporal patterns of Fucus distichus spp. edentatus (de la Pyl.) Pow. (Phaeophyceae: Fucales) in Central Puget sound. Botanica Marina 26:471-486. Thom, R. M. 1988. Benthic primary productivity in a Northwest eelgrass meadow. Journal of Phycology 24:26. Thom, R. M. 1990. Spatial and temporal patterns in plant standing stock and primary production in a temperate seagrass system. Botanica Marina 33:497-510. Thom, R. M. 1992. Accretion rates of low intertidal salt marshes in the Pacific Northwest. Wetlands 12:147-156. Thom, R. M., J. W. Armstrong, C. P. Staude, K. K. Chew, and R. E. Norris. 1976. A survey of the attached marine flora at five beaches in the Seattle, Washington, area. Syesis, 9, 267-275, (1976). Thom, R. M., and L. Hallum. 1991. Long-term changes in the areal extent of tidal marshes, eelgrass meadows and kelp forests of Puget Sound. Report FRI-UW-9008. Thompson, M., C. Hrabok, D. E. Hay, J. Schweigert, C. Haegele, and B. Armstrong. 2003. Juvenile herring surveys: methods and data base. Report 0706-6473, Department of Fisheries and Oceans Canada, Nanaimo, BC (Canada) Sci. Br. Thuringer, P., J. Harper, and B. Emmett. 2004. Mapping Nearshore Subtidal Biological and Physical Features in Victoria Harbour Using Towed Underwater Video Imagery. Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Toft, J. 2005. Benthic Macroinvertebrate Monitoring at Seahurst Park 2004, Pre-Construction of Seawall Removal. Technical Report. School of Aquatic and Fishery Science, Fisheries Research Institute, Washington University [Rep. Fish. Res. Inst. Wash. Univ.]:[np]. Toft, J., J. Cordell, and B. Starkhouse. 2005. Salmon Bay Natural Area Pre-Restoration Monitoring 2004. Technical Report. School of Aquatic and Fishery Science, Fisheries Research Institute, Washington University [Rep. Fish. Res. Inst. Wash. Univ.]:[np]. Toft, J., C. Simenstad, J. Cordell, and L. Stamatiou. 2004. Fish Distribution, Abundance, and Behavior at Nearshore Habitats along City of Seattle Marine Shorelines, with an Emphasis on Juvenile Salmonids. Technical Report. School of Aquatic and Fishery Science, Fisheries Research Institute, Washington University [Rep. Fish. Res. Inst. Wash. Univ.]:[np]. Toft, J. D., J. R. Cordell, C. A. Simenstad, and L. A. Stamatiou. 2007. Fish distribution, abundance, and behavior along city shoreline types in puget sound. North American Journal of Fisheries Management 27:465-480. Trimble, A., B. R. Dumbauld, and J. L. Ruesink. 2005. Restoration of native oyster (Ostreola concaphila) stocks in West Coast estuaries: Factors preventing recovery. Journal of Shellfish Research 24:337. Truscott, J. 2004. Coastal Planning in Georgia Basin: Baynes Sound and Malaspina Inlet Complex. Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Tularum, G. A., and M. Ilahee. 2007. Environmental concerns of desalinating seawater using reverse osmosis. J. Environ. Monitoring 9:805-813. Tullo, A. H., 2010. Eastman finds its stride. Chemical and Engineering News. p. 21-23, June 7, and Eastman expands 2-ethylhexanol, p. 31, September 27. Underwood, A. J. 1994. On beyond BACI: sampling designs that might reliably detect environmental disturbances. Ecological Applications 4:3-15. US Environmental Protection Agency. 2007. Reregistration Eligibility Decision (RED) for Mecoprop-p (mcpp) US Environmental Protection Agency. 2009. Contaminant Candidate List 3 – CCL. EPA 815-F-09-001. US Environmental Protection Agency. 2010. Inert ingredients permitted for use in nonfood use pesticide products last updated March 28, 2010. Office of prevention, pesticides and toxic substances. Van Alstyne, K. L., L. Koellermeier, and T. A. Nelson. 2007. Spatial variation in dimethylsulfoniopropionate (DMSP) production in Ulva lactuca (Chlorophyta) from the Northeast Pacific. Marine Biology 150:1127- 1135. Van Alstyne, K. L., J. J. McCarthy Iii, C. L. Hustead, and D. O. Duggins. 1999a. Geographic variation in polyphenolic levels of Northeastern Pacific kelps and rockweeds. Mar. Biol 133:371-379.

124 Van Alstyne, K. L., J. J. McCarthy, III, C. L. Hustead, and L. J. Kearns. 1999b. Phlorotannin allocation among tissues of northeastern Pacific kelps and rockweeds. Journal of Phycology 35:483-492. Van Alstyne, K. L., and K. N. Pelletreau. 2000. Effects of nutrient enrichment on growth and phlorotannin production in Fucus gardneri embryos. Marine Ecology Progress Series 206:33-43. Van Alstyne, K. L., K. N. Pelletreau, and K. Rosario. 2003. The Effects of Salinity on Dimethylsulfoniopropionate Production in the green alga Ulva fenestrata Postels et Ruprecht (Chlorophyta). Botanica Marina 46:350-356. Van Mooy, B. A. S., and R. G. Keil. 2002. Seasonal variation in sedimentary amino acids and the association of organic matter with mineral surfaces in a sandy eelgrass meadow. Marine Ecology Progress Series 227:275-280. Vanderhorst, J. R., J. W. Blaylock, and P. Wilkinson. 1979. Research to investigate effects from Prudhoe Bay crude oil on intertidal infauna of the Strait of Juan de Fuca. First annual report. Report, NOAA Environmental Research Labs, Boulder, CO (USA). Marine Ecosystems Analysis Project. Vermeer, K., R. W. Butler, and K. H. Morgan. 1994a. Comparison of seasonal shorebird and waterbird densities within Fraser River delta intertidal regions. Vermeer, K., K. H. Morgan, G. E. J. Smith, and A. N. Wisely. 1994b. Habitat use by waterbirds in the Cowichan River estuary. Visser, E. P., P. McDonald, and D. A. Armstrong. 2004. The Impact of Yellow Shore Crabs, Hemigrapsus oregonensis, on Early Benthic Phase Dungeness Crabs, Cancer magister, in Intertidal Oyster Shell Mitigation Habitat. Estuaries 27:699-715. Volkenborn, N., and K. Reise. 2006. Lugworm exclusion experiment: Responses by deposit feeding worms to biogenic habitat transformations. Journal of Experimental Marine Biology and Ecology 330:169-179. Waldichuk, M. 1983. Pollution in the Strait of Georgia: A review. Canadian Journal of Fisheries and Aquatic Sciences 40:1142-1167. Walsh, T. J., W. J. Gerstel, W. H. Graeber, and H. M. Shipman. 2002. Influence of intercepted landslides on nearshore habitat. Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Warner, L. C., and E. P. Visser. 2000. But the crabs keep coming: Trials and successes of the Grays Harbor Dungeness crab mitigation program. Journal of Shellfish Research 19:627. Washington State Department of Fish and Wildlife. 1993. 1992 Washington State salmon and steelhead stock inventory.in W. D. o. W. a. W. W. T. I. T. Washington Department of Fisheries, editor. Washington State Department of Ecology. 2006. Table 12, Summary of use, persistence, bioaccumulation potential for deca-BDE and deca-BDE alternatives. Final PBDE chemical action plan (CAP). Watabayashi, G., D. Heimer, and M. Hodges. 2002. Statistical trajectory analysis of the seeds of common cordgrass (Spartina anglica) in northern Puget Sound. Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Webber, H. H. 1979. The intertidal and shallow subtidal benthos of the west coast of Whidbey Island spring 1977 to winter 1978. Report, U.S. Environmental Research Laboratories, Boulder, CO. Marine Ecosystems Analysis Program. Webber, H. H. 1981. Growth rates of benthic algae and invertebrates in Puget Sound. 1: Literature review, and 2: Field studies on Laminaria and Nereocystis. Report, NOAA, Office of Marine Pollution Assessment, Boulder, CO (USA). Wekell, J. C., V. Trainer, D. Ayres, and D. Simons. 2000. The distribution of domoic acid concentrations in razor clams as a function of elevation between high and low tides at Kalaloch Beach Washington. Journal of Shellfish Research 19:638. Whitney, J., and D. Wildermuth. 2004. Assessment and management of intertidal clam resources in northern Puget Sound. Journal of Shellfish Research 23:659. Wieters, E. A., and S. A. Navarrete. 1998. Spatial variability in prey preferences of the intertidal whelks Nucella canaliculata and Nucella emarginata. Journal of Experimental Marine Biology and Ecology 222:133-148. Williams, H. F. L., and T. S. Hamilton. 1995. Sedimentary dynamics of an eroding tidal marsh derived from stratigraphic records of super(137)Cs fallout, Fraser Delta, British Columbia, Canada. Journal of Coastal Research 11:1145-1156. Williams, J. G. 1979. Estimation of intertidal harvest of dungeness crab, Cancer magister, on Puget Sound, Washington, beaches. Fish. Bull. 77:287-292. Williams, S. L., and M. H. Ruckelshaus. 1993. Effects of nitrogen availability and herbivory on eelgrass (Zostera marina ) and epiphytes. Ecology 74:904-918. Willis, P., B. Crespi, L. Dill, R. Baird, and M. Hanson. 2004. Natural hybridization between Dall’s porpoises (Phocoenoides dalli) and harbour porpoises (Phocoena phocoena). Canadian Journal of Zoology 82:828-834. Wilson, W. H. 1991. The effect of migratory shorebird predation on prey abundance at Grays Harbor, Washington. American Zoologist 31:103A.

125 Wissmar, R. C., and C. A. Simenstad. 1988. Energetic constraints of juvenile chum salmon (Oncorhynchus keta ) migrating in estuaries. Canadian Journal of Fisheries and Aquatic Sciences 45:1555-1560. Wonham, M. J., and J. T. Carlton. 2005. Trends in marine biological invasions at local and regional scales: the Northeast Pacific Ocean as a model system. Biological Invasions 7:369-392. Wood, W. A. 1996. Intertidal bivalve management on public tidelands in Puget Sound -- an overview. Journal of Shellfish Research 15:789. Woodruff, D., A. Borde, R. Garono, C. Simenstad, and J. Norris. 2004. Nearshore Habitat Mapping in Hood Canal Using Underwater Video and Hyperspectral Imaging. Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Wootton, J. T. 1991. Direct and indirect effects of bird predation and excretion on the spatial and temporal patterns of intertidal species. Dissertation. Wootton, J. T. 1995. Effects of birds on sea urchins and algae: A lower-intertidal trophic cascade. Ecoscience. Sainte-Foy 2:321-328. Wootton, J. T. 2002. Mechanisms of successional dynamics: Consumers and the rise and fall of species dominance. Ecological Research 17:249-260. Wootton, J. T., M. E. Power, R. T. Paine, and C. A. Pfister. 1996. Effects of productivity, consumers, competitors, and El Nino events on food chain patterns in a rocky intertidal community. Proceedings of the National Academy of Sciences, USA 93:13855-13858. Wootton et al. 2008 PNAS (TBA) Wright, J. T., S. L. Williams, and M. N. Dethier. 2004. No zone always greener: Variation in the performance of Fucus gardneri embryos, juveniles and adults across tidal zone and season. Marine Biology 145:1061-1073. Wyllie-Echeverria, S., A. Bailey, and B. Williams. 2004a. Changes to the Shoreline of Fidalgo Bay and Eastern Guemes Channel Since 1891: The Value of a GIS Approach. Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Wyllie-Echeverria, S., J. R. Cordell, J. R. Skalski, T. Klinger, M. Stamey, C. Young, K. L. Fresh, and T. Wyllie- Echeverria. 2003a. Seagrass Density and Abundance of Epibenthic Crustaceans: Implications for Outmigrating Juvenile Salmon in the Northeast Pacific. Gulf of Mexico Science 21:120-121. Wyllie-Echeverria, S., P. A. Cox, A. C. Churchill, J. D. Brotherson, and T. Wyllie-Echeverria. 2003b. Seed size variation within Zostera marina L. (Zosteraceae). Botanical Journal of the Linnean Society 142:281-288. Wyllie-Echeverria, T., D. O. Duggins, and S. Wyllie-Echeverria. 2004b. Evaluation of an Artificial Rock Reef for Colonization by Macroalgae. Puget Sound Action Team, PO Box 40900 Olympia WA 98504. Yao, T., S. Pond, and L. A. Mysak. 1985. Profiles of low-frequency subsurface current fluctuations in the Strait of Georgia during 1981 and 1982. Journal of Geophysical Research. C. Oceans 90:7199-7212. Yin, K., and P. J. Harrison. 2000. Influences of flood and ebb tides on nutrient fluxes and chlorophyll on an intertidal flat. Marine Ecology Progress Series 196:75-85. Young, C. M. 1985. Abundance patterns of subtidal solitary ascidians in the San Juan Islands, Washington, as influenced by food preferences of the predatory snail Fusitriton oregonensis. Marine biology , Heidelberg 84:309-321. Young, C. M. 1986. Defenses and refuges: Alternative mechanisms of coexistence between a predatory gastropod and its ascidian prey. Marine Biology , Heidelberg 91:513-522. Young, C. M., and F. S. Chia. 1982. Factors controlling spatial distribution of the sea cucumber Psolus chitonoides : Settling and post-settling behavior. Marine biology , Heidelberg 69:195-205. Young, C. M., and F. S. Chia. 1984. Microhabitat-associated variability in survival and growth of subtidal solitary ascidians during the first 21 days after settlement. Marine biology , Heidelberg 81:61-68. Young, D. R., R. J. Ozretich, J. D. Frazier, and S. F. Echols. 1993. PAH and PCB in water and intertidal mussels from Puget sound, W.A. Zacharias, M. A., D. E. Howes, C. Ogborne, and M. Morris. 1998. A biophysical habitat classification for intertidal environments in the Strait of Georgia. Report; Conference 0706-6457, Department of Fisheries and Oceans, West Vancouver, BC [Canada] Sci. Branch. Zacharias, M. A., M. C. Morris, and D. E. Howes. 1999. Large scale characterization of intertidal communities using a predictive model. Journal of Experimental Marine Biology and Ecology 239:223-242. Zardus, J. D. 1995. Influence of a deposit-feeding bivalve on species abundance and diversity in a subtidal soft- bottom community. Zisette, R., W. T. Trial, Jr., M. Vorass, and C. Patmont. 2002. Evaluating the effectiveness of capping mercury contaminated sediments at Eagle Harbor, Washington. Puget Sound Action Team, PO Box 40900 Olympia WA 98504.

126

Figures 1-3. Physical conditions over five annual cycles in the water column (200-2004, JEMS Program) just south of San Juan Island (source: Jan Newton), including salinity, dissolved oxygen, and temperature at three sites.

Figure 1

127

Figure 2

128 Figure 3

129 Figure 4. Mean temperature from Race Rocks, south of Victoria BC. This is the only location near the MSA that has a long-term temperature record. Note that a PDO shift occurred in 1977, accompanied by increasing temperatures, until 1999 when they began to decline again.

130 Figure 5. Map of all former and existing monitoring programs in San Juan County (MSA) and adjacent islands (from database in Appendix D)

131 Figure 6. Map of all former and existing monitoring programs in San Juan County (MSA) and adjacent islands (from database in Appendix D), with ending date displayed.

132

Figure 7. Map of all former and existing monitoring programs in San Juan County (MSA) and adjacent islands (from database in Appendix D), with managing organization displayed.

133 Figure 8. Map of all former and existing monitoring programs in San Juan County and adjacent islands (from database in Appendix D), with targets and threats displayed.

134 Appendix A. DRAFT Ranking Matrix (See Excel listing, separate)

Appendix B. Criteria Lists • Required Monitoring – agencies that require San Juan County to monitor. Local – Stormwater Utility, other State – Critical Areas Ordinance, Shoreline Master Plan, Growth Management Act Federal – Endangered Species Act Recovery Plans, other

• Enforcement Component – county departments, state/federal agencies that have enforcement authority SJC Sheriff’s Department SJC Code Enforcement Officer Town of Friday Harbor Code Enforcement Officer WA State Department of Ecology Washington State Department of Fish & Wildlife US Fish & Wildlife

• Relevant Plans or Legislation – plans or legislation that call for monitoring; REQ indicates that monitoring is required. REQ – ESA Recovery Plans (Chinook salmon, southern resident orcas, others) REQ – On-site Sewage Systems, the “Sewage Bill" (WAC 246-272A-0015) REQ – SJC Chapter of the Puget Sound Chinook Salmon Recovery Plan Voluntary - SJC Action Agenda (Puget Sound Action Plan); San Juan Action Agenda Profile REQ – SJC Critical Areas Ordinance REQ – SJC Habitat Conservation Plan Voluntary - SJC Marine Stewardship Area Plan; MSA Monitoring Plan REQ – SJC Shoreline Master Plan REQ – SJC Water Resources Management Plan (WRIA 2) REQ – SJC Stormwater Utility REQ – WA State Heritage Program (native ecosystems and rare species) REQ – Water Systems: Eastsound, Rosario, Roche Harbor, Town of Friday Harbor; 34 smaller water systems in SJC

• Ecosystem Benefit, Priority Area and/or Target – specified in the plans listed in Appendix F, References, or in noted Washington State programs. SJC Action Agenda (currently being updated by the local Implementation Committee) Nearshore Chinook salmon Eelgrass and Seagrasses Feeder bluffs Forage fish (surf smelt and sand lance) Kelp Priority Habitats and Species (DNR) Rookeries Rocky reefs

135 Shellfish WA State Species of Concern (WDFW) Marine Marbled murrelet feeding areas Priority Habitats and Species (DNR) Southern resident orca WA State Species of Concern (WDFW) Freshwater/Terrestrial Coastal prairies Freshwater sources Old growth areas Priority Habitats and Species (DNR) Soils (agricultural soils in particular) WA State Species of Concern (WDFW) Wetlands SJ Chapter of the Puget Sound Chinook Salmon Recovery Plan - Salmon and fish bearing streams SJC Habitat Conservation Plan Habitat Conservation Areas– 17 in the county Habitat Conservation Priority – shorelines, large intact forests, coastal prairies, oak woodlands, high quality wetlands SJC Pilot Stormwater Monitoring Plan - Stormwater Monitoring Sites SJC Marine Stewardship Area Plan Bottomfish Recovery Zones Pacific salmon and forage fish Marine mammals Marine Preserves Nearshore sand, mud and gravel communities Rockfish, lingcod and greenling Rocky subtidal communities Rocky intertidal communities Seabirds SJC Watershed Management Action Plan & Characterization Report Priority Watersheds– 13 in the county Wellhead Protection Areas Drinking Water Protection Areas Groundwater Recharge Areas WA Department of Ecology - Shellfish beds WA Department of Fish & Wildlife - WA State Species of Concern WA State Department of Natural Resources (DNR) - Priority Habitats and Species WA Natural Heritage Program Priority Plant Communities Rare Plants National Oceanographic & Atmospheric Administration - Whalewatch Exclusion Zone

136 • Beneficial Uses – beneficial uses related to water quality and quantity in marine &/or surface waters as defined in WAC 173. Aquatic life (marine waters) Shellfish harvesting (marine waters) Domestic, industrial and agricultural water supply (surface waters) Salmonid spawning, rearing & migration (surface waters) Stock watering (surface waters) Aesthetic values (marine and surface waters) Boating (marine and surface waters) Commerce & navigation (marine and surface waters) Harvesting (marine and surface waters) Recreation (marine and surface waters) Wildlife habitat (marine and surface waters)

• Threats/Stressors – threats or stressors that are specified in plans listed in Appendix F, References. Agriculture (if mismanaged) Altered hydrology Anchoring (if mismanaged) Aquaculture (if mismanaged) Climate change – changes in sea level, temp, precip, sea surface temp, ocean acidification Derelict gear Erosion and/or sedimentation Excess nutrients Fire suppression (if mismanaged) Habitat fragmentation Harvest pressure (if mismanaged) Impervious surfaces – parking lots, roads, driveways, roofs, lawns Invasive species Loss of biodiversity Loss of population numbers Oil spills and leakage Pollutants – to freshwater, marine, nearshore and terrestrial environments Pathogens Recreational trampling of sensitive habitats Runoff from built environment (if mismanaged) Seawater intrusion Shoreline alteration (if mismanaged) Soil compaction Timber harvest (if mismanaged) Toxins – metals, PAHs, pyrethroids, surfactants, persistent bioaccumulative toxins Vegetation removal (if mismanaged) Vessel noise and traffic Water withdrawals (if mismanaged)

137 Appendix C. Actual and Potential Partners

• Local agencies, county departments, and municipalities – Port of Friday Harbor, SJC Beach Watchers-WSU, SJC Environmental Health & Community Services, SJC Community Development & Planning Department, SJC Land Bank, SJC Lead Entity for Salmon Recovery WRIA 2, SJC Marine Resources Committee, SJC Public Works, SJC Stormwater Utility, San Juan Islands Conservation District, School Districts, Town of Friday Harbor • Local advisory boards and committees – Open Space Advisory Team, Stormwater Advisory Board, Water Resources Management Committee • Local NGOs – Beam Reach, Chambers of Commerce (Orcas and San Juan), Center for Whale Research, Friends of the San Juans, Kwiaht, Orcas Island Community Foundation, Private Schools, San Juan Community Foundation, San Juan Nature Institute, SJ Preservation Trust, The Whale Museum/Soundwatch Program • Regional agencies and efforts – Estuary and Salmon Restoration Program, Northwest Straits Commission, Puget Sound Ambient Monitoring Program, Puget Sound Ecosystem Restoration Project, Puget Sound Partnership, Skagit Fisheries Enhancement Group • Regional NGOs – People for Puget Sound, SeaDoc Society, The Russell Family Foundation • Tribal governments – Lummi Nation, Swinomish Indian Tribal Community, Tulalip Tribes, Samish Nation • Academic institutions – Skagit Valley College, UW (Friday Harbor Labs, School of Marine Affairs, various departments), Western (Huxley Environmental College, Shannon Point Marine Lab), WSU, others • State/Federal NGOs – Audubon, National Fish & Wildlife Foundation, The Nature Conservancy, Reef Environmental Education Foundation, Wild Fish Conservancy NW (WA Trout), Washington Water Trust • State agencies – Department of Commerce, Department of Health, Department of Ecology, Department of Fish & Wildlife, Department of Natural Resources, Recreation and Conservation Office, Sea Grant • Federal agencies – Army Corp of Engineers, Bureau of Land Management, Environmental Protection Agency, National Marine Fisheries Service, National Oceanographic & Atmospheric Administration, National Park Service, National Science Foundation, US Fish & Wildlife Service, US Geological Survey • Community monitoring partners – local landowners, businesses, marinas, resorts, service organizations, Chambers of Commerce, Trails Committee, sailing and yacht clubs, Waldron Citizen Science, Lopez Community Salmon Team, Marine Health Observatories (Indian Island, Friday Harbor, Fisherman’s Bay)

138 Appendix D. Database constructed for this Monitoring Plan, including all former and current monitoring efforts within the MSA (see also complete Excel version).

organization general specific methods start_date end_date monitoring_frequency                                                                                                                                                                                                                                                                                                                                                                                                                                                              139

•

Appendix E. Indicators and Key Attributes for Pacific Salmon from CAP Workbook (next page)

* The Juvenile Prey Base Protection project by KWIAHT will assess the prey resources utilized by juvenile Chinook. A companion project to the Habitat Based Assessment of Juvenile Salmon (Big Picture) project as it will obtain gastric contents from Chinook collected via the Big Picture sampling.

140 Key Attribute Organization References Current performing by Target Monitoring or Duration / Indicator monitoring (w/ current Assessment Frequency and/or indicator Information assessment status) abundance of juvenile herring - Pacific - Herring WDFW Annually indicator is interior San Juans salmon spawning herring stock status assessment -Condition: surveys prey - Stock Status abundance Assessment for resident Chinook (depressed (34% of 25 year mean)) abundance of juveniles by Pacific - No data Skagit River Sampling species (to be decided) salmon currently System will occur -Size: available. Cooperative monthly juvenile - WRIA2 over the 3 salmon Habitat Based year study population Assessment of from 2008 abundance Juvenile - 2010. (no data) Salmon (Big Picture) project will provide data on juvenile salmonid utilization by habitat type. Will also provide genetic analysis to determine which stocks and species are present. availability of brackish habitat per Pacific 2004 DNR once in PSAT method salmon characterization 2004 -Condition: of the availability of distribution, brackish type and habitat amount of (physiological historical tidal dependency) wetlands. (San Juans Wetland losses currently were assessed rated as for both loss of 'medium' by area and loss of PSAT) units. crab Pacific - No data larvae/amphipod/zooplankton salmon currently indicator -Condition: available. abundance of - *Note: prey prey items for study (see salmon up to below)

141

Appendix F. Reference Documents for Monitoring Strategy (Part I)

• Interim Aquifer Protection Report, Eastsound, San Juan County, December 2008, Pacific Groundwater Group • Marine Stewardship Area Monitoring Plan, DRAFT, December 15, 2009, SJC Marine Resources Committee • SJC Action Agenda • SJC Chapter of the Puget Sound Chinook Salmon Recovery Plan, Puget Sound Shared Strategy, June 2005 • SJC Habitat Conservation Plan 2008-2014, SJC Land Bank • SJC Marine Stewardship Area Plan • SJC Nearshore Impact Assessment, June 2006, Friends of the San Juans • SJC Pilot Stormwater Monitoring Plan, DRAFT, March 2010, Stillwater Sciences • SJC Watershed Management Action Plan & Characterization Report, Final approved August 24, 2000, SJC Health & Community Services

142