Fishery Analysis for the Carmel River Lagoon Biological Assessment Report

March 2014

Prepared By:

P.O. Box 200, Brookdale, CA 95007

Prepared For:

Monterey County Resource Management Agency Monterey County Government Center 168 W. Alisal Street, 2nd Floor Salinas, CA 93901 TABLE OF CONTENTS

INTRODUCTION ...... 1 Project History ...... 1 Memorandum of Understanding ...... 4 Project Description ...... 5 EPB Components ...... 6 SRPS Components ...... 6 ISMP Components ...... 6 Project Action Area ...... 8 STUDY METHODS ...... 9 Listed Fish Species...... 9 ENVIRONMENTAL SETTING ...... 10 Impacts of Historical Mechanical Breaching ...... 10 Benefits of a Natural Breaching Regime ...... 11 Steelhead Occurrences in the Project Area ...... 12 Adult Migration ...... 13 Spawning ...... 17 Summer Rearing ...... 17 Smolt Migration ...... 18 Physical and Biological Aspects of the Carmel Lagoon/Estuary Pertaining to Steelhead Habitat and Rational for Assessing Impacts of Proposed Actions ...... 24 Food Web ...... 24 Water Temperature ...... 24 Oxygen Levels ...... 25 Discussion of Critical Environmental Factors ...... 26 DISCUSSION OF SOUTH-CENTRAL CALIFORNIA COAST STEELHEAD DPS ...... 36 Survey Results ...... 36 Critical Habitat ...... 36 Avoidance and Minimization Efforts ...... 36 Project Effects ...... 38 EPB ...... 38 SRPS ...... 39 ISMP ...... 40 Project Impacts ...... 40 Impacts potentially resulting from the EPB: ...... 40 Impacts potentially resulting from the SRPS ...... 41 Impacts potentially resulting from the ISMP ...... 41 Modifications to the Project to Mitigate Potentially Negative Effects ...... 42 Monitoring and Reporting ...... 44 DRAFT Fishery Analysis for The Carmel River Lagoon Biological Assessment Report− January 2014 D.W. ALLEY & Associates Page i

Reporting Recommendations ...... 46 Cumulative Effects (ESA) ...... 46 CONCLUSIONS AND DETERMINATIONS ...... 47 Conclusions ...... 47 Determination...... 47 LITERATURE CITED ...... 48 LIST OF CONTACTS AND PERSONAL COMMUNICATIONS ...... 52 APPENDIX A: Interim Sandbar Management Plan (ISMP) APPENDIX B: California Department of Fish and Game Avoidance and Minimization Measures

DRAFT Fishery Analysis for The Carmel River Lagoon Biological Assessment Report− January 2014 D.W. ALLEY & Associates Page ii

FIGURES Figure 1. Project Location ...... 2 Figure 2. Project Components ...... 7 Figure 3. Steelhead Occurrences Within the Vicinity ...... 37

CHARTS Chart 1. Carmel River Mean Daily Flow at First Mechanical Breach of Sandbar Barrier, 1993─2012. Data from Balance Hydrologics Technical Memorandum (2013)...... 16 Chart 2. Actual Daily and Cumulative Smolt Catch Over Time Below Los Padres Dam, 1999...... 20 Chart 3. MPWMD Steelhead Smolt Trapping – Scarlett Site, 2007...... 21 Chart 4. MPWMD Steelhead Smolt Trapping – Scarlett Site, 2013...... 21 Chart 5. San Lorenzo River Smolt Trapping, 1987...... 22 Chart 6. San Lorenzo River Smolt Trapping, 1988...... 22 Chart 7. Morning Oxygen Levels and Gage Heights in the Central Embayment of the Carmel Lagoon/Estuary, 2005...... 29 Chart 8. Morning Oxygen Levels and Gage Heights in the South Arm of the Carmel Lagoon/Estuary, 2005...... 30 Chart 9. Morning Oxygen Levels and Gage Heights in the North Arm of the Carmel Lagoon/Estuary, 2005...... 31 Chart 10. Morning Water Temperature and Gage Heights in the Central Embayment of the Carmel Lagoon/Estuary, 2005...... 32 Chart 11. Morning Water Temperature and Gage Heights in the South Arm of the Carmel Lagoon/Estuary, 2005...... 33 Chart 12. Morning Water Temperature and Gage Heights in the North Arm of the Carmel Lagoon/Estuary, 2005...... 34

TABLES Table 1. Carmel Lagoon First Seasonal Breach (FSB) of Each Year...... 14 Table 2. Carmel Lagoon Breaching Events and Days Open to Ocean...... 15 Table 3. Historical Record of Natural Sandbar Closure at Santa Rosa Lagoon (1993–2007) with Groundwater Wells Influencing Streamflow in Drier Years (from Alley 2008)...... 23 Table 4. Criteria for rating water quality measurements within 0.25 Meters of the bottom or at 1 meter if salinity stratification caused oxygen depletion at greater depth (from Alley 2013a)...... 27

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INTRODUCTION

The Proposed Action would be located within the Carmel River Lagoon located between State Route (SR) 1 and the Pacific Ocean in the unincorporated Carmel area of Monterey County, California (Figure 1). The Carmel River drains approximately 246 square miles of the Santa Lucia and Sierra de Salinas Mountains into the Carmel Bay. About 270 acres of the Carmel River Beach and Lagoon are owned by the State of California/California Department of Parks and Recreation (State Parks). Other property owners within the Lagoon include Carmel Area Wastewater District (16 acres), Carmel Unified School District (9 acres), City of Carmel-by-the-Sea (6 acres), and Homestead Inn/Mission Ranch (16 acres).

The Carmel Lagoon Ecosystem Protective Barrier (EPB), Scenic Road Protection Structure (SRPS), and Interim Sandbar Management Plan (ISMP) Project (hereafter referred to as Project) is a comprehensive plan meant to promote improvement in ecological function of the Carmel Lagoon, including natural floodplain function and improvement of habitat for threatened and endangered species within the existing lagoon by allowing the lagoon to breach naturally, without increasing flood risk to private structures and public facilities. The EPB would maintain existing protection from flooding to low-lying homes and other local Carmel-by-the-Sea infrastructure along the north edge of the Lagoon in the context of a reduction in the frequency of mechanical management of the sandbar. The SRPS would provide protection along the northern sand cliffs from erosion associated with lagoon-ocean processes that might occur if sand bar management were to cease. The ISMP is an interim sand bar management plan meant to provide a short- term solution to potential flooding issues with select sand bar breaching actions that allow additional natural function in the lagoon while still protecting properties and infrastructure, with the understanding that the development of the EPB and SRPS lead to potential long-term solutions that returns the Lagoon, its sand bar, and associated riverine and ocean dynamics to more natural cycles.

Project History The Carmel River Lagoon, located at the mouth of the Carmel River, is a very productive estuary which serves as rearing habitat for juvenile, federally listed South-Central California Coast steelhead Distinct Population Segment (S-CCC steelhead; Oncorhynchus mykiss). The Carmel River was designated as critical habitat for steelhead in September 2005. The ecosystem in and around the Carmel River Lagoon also supports other federally listed species such as the California red-legged frog, western snowy plover, and Smith’s blue butterfly, and numerous other special-status species.

The Carmel River Watershed has very large variations in seasonal and yearly discharge rates. The lagoon is not connected to the ocean during times of low or no river flow, when ocean waves build a barrier beach (sandbar) across the mouth of the lagoon and close to the lagoon’s outflow channel. When river inflow is relatively low, equilibrium is reached between river and groundwater inflow, outflow through the barrier beach and evapotranspiration. When river flow increases in the fall and early winter, lagoon water levels can rise to flood stage, with the result that private properties along the northern edge of the lagoon, as well as a parking lot and restroom facility owned by State Parks, are threatened with flooding before the sandbar would open naturally.

Since at least the early 20th century, when water in the lagoon rose to levels that threatened private property, the sandbar has been mechanically managed (breached) in order to lower the lagoon’s water Fishery Analysis for The Carmel River-Lagoon Biological Assessment Report – January 2014 D.W. ALLEY & Associates Page 1

mi 02.5 5 10

km 02.5 5 10

^_ Project Location

Figure N Vicinity Map 1 level to below flood stage. Since 1973, emergency sandbar management was carried out by the County of Monterey (County), Monterey County Water Resources Agency (MCWRA), and State Parks.

In 1992, regulatory agencies informed the County that its ongoing sandbar management did not qualify as emergency actions due to the predictability of flooding at Carmel River Lagoon. In response, the County prepared an Interim Sandbar Management Plan and Beaching Criteria and submitted it to the various regulatory agencies. In 2003 NMFS drafted a Draft Jeopardy Opinion (JO) in response to the proposed Interim Sandbar Management Plan. The County updated the agencies in the years following; however, a concern about lack of supporting data and analysis was expressed by the agencies and sandbar management continued without permits. In 2005 the Carmel River Lagoon Technical Advisory was formed to make recommendations for research with the hope to develop better strategies for breaching.

The motivation to pursue a project occurred in January 2005 when the County graded an outlet channel along a “non-traditional” north-northwesterly alignment based on consultation with National Oceanic and Atmospheric Administration National Marine Fisheries Service (NMFS). The intent was that this new channel alignment would result in a decrease in both the rate of lagoon draw-down and a reduction in the total drop in lagoon level thereby reducing impacts to federally listed steelhead and critical habitat. The breach was considered by some to be a success, as the new, longer breach channel was able to moderate flow rates and total volume of draw-down.

In October 2010, the Carmel River Steelhead Association (CRSA) filed a 60-day notice of intent to sue the County for violating the federal Endangered Species Act (ESA), and advised the County to take whatever legal steps that may be necessary to prevent the County from engaging in unauthorized take of steelhead. After this 60-day notice, the County engaged in discussions with NMFS regarding obtaining the U.S. Army Corps of Engineers (USACE) permit for their breaching program and subsequent biological opinion from NMFS. In November 2010, NMFS agreed to work with the County to establish milestones in the development of alternatives to mechanical breaching, and encouraged them to comply with federal law by obtaining the necessary permits. Subsequent to this event, NMFS and the Corps indicated that no additional emergency permits would be issued to breach the lagoon unless a long-term solution was developed. This agreement was presented to the CRSA by the County in an effort to prevent continued legal action.

In winter of 2011, efforts to channel toward the north end of the beach resulted in flood damage due to significant river flows and extremely high tidal and wave conditions, which pushed the river outlet channel closer to the bluffs. While the County made several efforts to redirect the channel, the actions ultimately resulted in significant sand loss and widening of the mouth further. The channel scoured the base of the bluff supporting Scenic Road, to the point that road stability was threatened, and washed away a significant portion of the Carmel River State Beach parking lot and very significantly undermined the park’s restroom building. The State Beach parking lot provides primary access to the beach for the public and for emergency response. Scenic Road is critical because, in addition to providing public access to the State Beach, it is the sole access to six private homes, and contains public utilities, including water and sanitary sewer. Damage to the restroom and/or sewer lines could pose a significant environmental risk.

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Memorandum of Understanding In 2010, the MCWRA submitted an application to the USACE for a permit to manage the sandbar. In September 2011, the Monterey County Resource Management Agency (RMA) assumed a lead role for the Carmel Lagoon management. The USACE consulted with the NMFS through the required section 7 consultation process under the federal ESA. During the consultation process, the NMFS affirmed that annual mechanically breaching as proposed in the permit application would likely adversely affect S-CCC steelhead and destroy and adversely modify its critical habitat, and, therefore, a Jeopardy Opinion (JO) would be issued. The original JO determination was first drafted in 2003, and since no changes to the breaching plan were made, it was reaffirmed in 2011. A meeting with the NMFS and USACE to better define a solution to mechanical breaching was subsequently held. During the meeting is was identified that the EPB and SRPS projects were developed within the 2011 draft JO as reasonable and prudent measures and are now the preferred projects with a means to achieving the following objectives: . To improve the functions and values of the ecosystem in and around the Lagoon by allowing lagoon levels to rise and the lagoon to breach naturally (versus mechanically breaching the Lagoon) . To reduce potential flood risks for existing public facilities and private structures in the low-lying developed areas located immediately to the north of, and within, the Lagoon as a result of predicted sea level rise during the next 50 years and reduction in mechanical breaching. . To protect public infrastructure (e.g., Scenic Road embankment, State Parks restroom and parking facilities) from storm surge and scour resulting from a northerly-aligned channel.

The USACE and NMFS informed the MCWRA and County that issuance of a JO could be avoided if the application was withdrawn and a new application was filed for the EPB and SRPS projects. Therefore, the County withdrew its application for long-term sandbar management, and submitted new applications to all permitting agencies for approval of the EPB and SRPS projects, as well as a 5-year Interim Sandbar Management Plan, while the County completes the plans and construction of the projects.

In an effort to reduce impacts of mechanical breaching during the development and implementation of the regulatory agency preferred project, RMA worked with the USACE to develop a draft Memorandum of Understanding (MOU) that would include the USACE, County, and NMFS as signatory agencies. This document was reviewed by the USFWS as a consulting agency to the USACE. In September 2011, a draft MOU was completed for management of the Carmel River Lagoon. The MOU: . Establishes a long-term plan to balance protection of private property with protection of federally listed species . Recognizes that mechanical managing the Carmel River Lagoon over the long run was not in the best interest of the County, USACE, and NMFS . Identifies two long-term solutions as alternatives to performing sandbar management: the EPB and the SRPS . Agrees to allow an Interim Sandbar Management Plan (ISMP) for temporary (5 years) management of the sandbar while the County develops the EPB and SRPS projects (design, environmental review, and construction)

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The MOU was approved by the Monterey County Board of Supervisors on June 11, 2013.

Project Description . The Proposed Action involves implementing three project components: 1) Ecosystem Protective Barrier (EPB); 2) Scenic Road Protection Structure (SRPS); and 3) Interim Sandbar Management Plan (ISMP). The Proposed Action would be located within the Carmel River Lagoon located between State Route (SR) 1 and the Pacific Ocean in the unincorporated Carmel area of Monterey County, California (Figure 1). The project components are located within the following areas (Figure 2):EPB – Carmelo Street between the State Parks parking lot and 17th Avenue and continuing east along the southern boundary of the Fourth Addition neighborhood (between 16th and 17th Avenues) terminating at the eastern boundary of the Carmel River Elementary School property; . EPB (Alternative) – If the EPB/SRPS projects are determined to impact operations of the Mission Ranch, the EPB would continue from the eastern boundary of the Carmel River Elementary School and extend east across a sheep pasture to the southern boundary of Mission Ranch development and continuing to the east side of the tennis courts; . SRPS – toe of slope of the embankment to Scenic Road, from approximately Valley View Avenue to the southern end of the State Parks parking lot; and . ISMP – various management activities within the Carmel River and Lagoon.

The objectives of the EPB project are: 1. To improve the functions and values of the ecosystem in and around the lagoon by allowing lagoon levels to rise and the lagoon to breach naturally, thereby allowing for conditions most conducive to the establishment of a perched hydrologic morphology within the lagoon, versus mechanically breaching the lagoon which results in lower water levels and negative impacts to fish and wildlife. 2. To maintain the current level of flood protection for existing public facilities and private structures in the low-lying developed areas located immediately to the north of, and within, the Lagoon as a result of predicted sea level rise during the next 50 years and reduction in mechanical breaching.

The objectives of the SRPS project are: 1. To protect public infrastructure (Scenic Road embankment, State Parks restroom, and parking facilities) from scour resulting from a northerly-aligned lagoon outflow channel that may result from a reduction in mechanical breaching. 2. To protect the Scenic Road embankment from the increasing risk of erosion resulting from ocean storm surge in the context of global warming.

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The objective of the ISMP project is: 1. To reduce potential impacts to the maximum extent possible to both wildlife and property during the interim period while planning and implementation for the EPB and SRES moves forward.

EPB Components The proposed EPB alignment includes a setback of up to 40-feet from the property line with a top of wall elevation of 17.5 feet based on the North American Vertical Datum of 1988 (NAVD88). This option was recommended as a component of the Preferred Alternative because it: . increases protection of facilities and homes accounting for sea level rise over the next 50 years; . minimizes ecological impacts by eliminating drainage infrastructure and fill; . minimizes visual impacts with a lower height and greater area of vegetative cover; . reduces noise because of smaller pumps with less frequent pumping; and . increases area that serves as a bioswale to collect urban runoff.

If the proposed project is determined to impact operations of the Mission Ranch, a separate EPB alignment would continue from the eastern boundary of the Carmel River Elementary School and extend across the southern boundary of Mission Ranch development.

SRPS Components The Feasibility Report evaluated four different alignments and designs ranging from riprap at the toe of slope to a pile wall located at the top of slope (edge of right-of-way). SRPS Alternative 1 – Revetment (Rip Rap) Located at Toe of Slope was determined to be the Preferred Alternative. This proposed SRPS involves excavation of the beach that would be followed by installation of a geotextile, then by two layers of armor rock. The excavated sand would be replaced back on to the armor rock, which would be ½- to 1- ton sized rock.

The Feasibility Report determined that rip rap provides the most natural material and the structure would be covered with sand when the beach is not breached. The alignment allows continued use of the beach area located north of the barrier when (and if) the beach breaches to the north.

ISMP Components The County is seeking permits for a long-term solution that would avoid performing mechanical breaching for flood control purposes. The process to complete technical feasibility studies, design, environmental review, permitting, and construction is estimated to take up to eight years, depending on resource availability; however, the County is making every effort to reduce this timeframe to five years or less. In the interim, the County has developed the ISMP for managing the Lagoon including winter openings and summer closure in the best possible manner that reduces potential impacts to both wildlife and property.

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Source: Whitson Engineers, 2013 CARMEL RIVER LAGOON ENVIRONMENTAL PROTECTIVE BARRIER AND SCENIC ROAD PROTECTION STRUCTURE Project No.: 2487.03 Whitson Engineers Figure PROPOSED PROJECT SUMMARY MAP 9699 Blue Larkspur Lane | Suite 105 | Monterey, CA 93940 | 831 649-5225 | F 831 373-5065 AUG 7, 2013 Project ComponentsCIVIL ENGINEERING L AND SURVEYING PROJECT MANAGEMENT | www.whitsonengineers.com 1"=250' MONTEREYN COUNTY NEAR CARMEL, CALIFORNIA Sheet 1 of 1 2 The ISMP generally includes the following (a copy of the ISMP is included in Appendix A): 1. Sand bags: As a first course of action ahead of the rain season, generally defined as October 15, and before mechanically managing the sandbar, the County will stockpile sand and place sand bags along the property boundary of State Parks and homes along the north end of the Carmel Lagoon (Camino Real, River Park Place, Monte Verde Street, and 16th Avenue). This action is subject to receiving permission from all of the property owners. The County will make it clear to homeowners that management of the sandbar is a last resort and that sandbag placement is a crucial component of flood control. 2. Public Outreach: The County will initiate public outreach to warn homeowners so they take appropriate precautions to protect their property during the rainy season (October 15 – April 15). Public outreach will include education on the effect of manual breaches completed by members of the community. This is a carefully managed system and unpermitted manual breaches are extremely harmful and illegal. The County will also make best efforts to keep interested parties informed of actions taken through the rain season; however, the County’s first priority is communication with the USACE and NMFS. 3. Sandbar management: The County, after receiving appropriate approvals from permitting agencies, will manage the sandbar for flood protection (e.g., mechanical breaching). Any such work would be performed only when necessary – based on pre-determined river and/or tide conditions – to prevent flooding of homes and would be implemented in a manner that would minimize impacts to S-CCC steelhead and their habitat. 4. Re-establishment/Summer Management: The County would assure any outlet channel work performed during the winter is closed off and the sandbar restored at the conclusion of the rain season.. The intent of the summer sandbar channel closure is to promote habitat for listed species throughout the summer months. When or if the level of water subsides in the Carmel Lagoon so that areas are dewatered and there are adequate quantities of sand located on the beach, the County may harvest sand from the beach to restore the beach.

Project Action Area The project area extends from the barrier beach inland toward Highway 1 into the main embayment of the lagoon/estuary, the north and south arms and submerged wetlands (semi-permanent and seasonal marsh) at the periphery of open water. The Carmel Lagoon/Estuary is designated critical habitat for steelhead by the National Marine Fisheries Service (NMFS). The project area for fish expands and contracts with fluctuating water surface elevation (WSE), which is dependent on the physical conditions of the barrier beach (sandbar). When the sandbar is closed to the ocean and stream inflow exceeds seepage rate through the sandbar as occurs at the beginning of the rainy season with stormflow, WSE and lagoon area-volume- depth increase and expand into the semi-permanent and seasonal marshland. If the infiltration rate exceeds stream baseflow and underflow with a closed sandbar as occurs at the end of the rainy season after stormflows end, the WSE declines along with lagoon area, volume and depth through the dry season, leaving limited permanent marsh at the periphery of open water. The lagoon WSE, area, volume and depth typically increase in fall from tidal overwash.

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STUDY METHODS

The technical information contained in this document is a compilation of a comprehensive literature review and professional experience. The analysis includes review of documents specific to the resource within its range as well as documents prepared for the project, personal communication with regulatory and responsible agency staff and scientific experts.

Assessment of habitat conditions and potential steelhead use of Carmel Lagoon/Estuary were determined by previous data collection. Timing of steelhead smolt migration in the Carmel River was assessed from smolt trapping efforts by the Monterey Peninsula Water Management District (MPWMD) in 1999, 2007 and 2013, with additional smolt trapping data collected by Don Alley and Stafford Lehr in 1987-88 in the San Lorenzo River, Santa Cruz County. Steelhead lagoon use was assessed from Carmel Lagoon fish sampling by Don Alley in 1996, fish sampling by Kevan Urquhart (MPWMD) at Carmel Lagoon, snorkeling and visual observations by David Dettman (MPWMD), soundings made by California State University at Monterey Bay (CSUMB) students and underwater video observations by J. Larson et al. at CSUMB. Lagoon water quality data were evaluated from MPWMD (WY2004-2013), Alley (WY1997) and Lumas (WY2005). The project description was provided by Denise Duffy & Associates. Projects were described in detail with alternatives in the feasibility report completed by Whitson Engineers, Moffat Nichol and H.T. Harvey & Associates. Technical memoranda were evaluated from our consultant team- Whitson Engineers, Balance Hydrologics, Inc. and Moffat Nichol regarding barrier beach dynamics as a function of streamflow and flood control measures and regarding relationships between lagoon/estuary area, volume and depth as function of water surface elevation. Additional recent emails and conversations with experts regarding physical dynamics, habitat use and biological assessment of Carmel Lagoon and other lagoons occurred with Ed Ballman, Beverly Chaney, David Dettman, Carlos Garza, Larry Hampson, Josh Harwayne, Brian LeNeve, Jacqueline Pearson-Meyer, Nathaniel Milam, Ed Morrison, Carl Schreck, Anne Senter, Jerry Smith, Dilip Trivedi and Kevan Urquhart (See list of contacts and personal communications after Literature Cited).

Listed Fish Species The S-CCC steelhead were listed as federally threatened in 1997, re-listed again as threatened in 2006, and includes all naturally spawned populations of steelhead in streams from the Pajaro River to, but not including, the Santa Maria River (NMFS 2006). Critical habitat for the DPS was designated in 2005 and includes the Carmel River Lagoon (NMFS 2005). Steelhead are also a California Species of Special Concern. Tidewater goby (Eucyclogobius newberryi) is federally endangered but was previously extirpated from Carmel River Lagoon (Swift et al. 1989). It was undetected during October 1996 sampling of Carmel River Lagoon (Alley 1997). Other non-listed, native fish species captured in Carmel River Lagoon include threespine stickleback (Gasterosteus aculeatus), staghorn sculpin (Leptocottus armatus) and starry flounder Platichthys stellatus). Non-native species captured were hitch (Lavinia exilicauda; California native but not in the Carmel River) (Alley 1997) in the lagoon and striped bass (Morone saxatilis) in the estuary (Kevan Urquhart, pers. comm. 2011).

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ENVIRONMENTAL SETTING

Impacts of Historical Mechanical Breaching Once fall storms begin, stream inflow to Carmel Lagoon increases, the lagoon becomes deeper, cooler and less saline. However, this period may be abbreviated if inflow greatly exceeds seepage rate through the sandbar and evaporation rate. Under existing conditions, lagoon WSE increases rapidly to threaten flooding if expected to rise above 12.74 feet. The lagoon has historically been breached (20 of the last 21 years) to prevent flooding. Breaching converts the lagoon to an estuary connected to the ocean and opens it up to daily fluctuations in tidal cycles. The estuary WSE rapidly declines within hours with loss of estuary area, volume and depth. The speed of estuary evacuation after the breach depends on the degree of erosion occurring to the outlet channel. Evacuation begins slowly and increases as the outlet channel erodes and enlarges. Factors that increase erosion include the high stormflow intensity, deep notching in the beach to direct the outflow, breaching on an outgoing tide, shorter length of the outlet channel to make breaching more perpendicular to the barrier breach and higher swell to cause more beach erosion. The lowest estuary WSE reached after a breach is typically 5.24−5.74 feet (NAVD88), and is likely the result of the estuary being reduced to a river channel flowing directly out to sea past the south arm at the existing stream gradient (James 2005).

The initial mechanical breach of the rainy season results in significant steelhead habitat loss, and juvenile steelhead exit to the ocean. If the breach occurs just prior to the expected natural breach under high stormflow conditions, the impact is insignificant. However, if the mechanical breach occurs at low stormflows that would have likely delayed a natural breach from 5 days to weeks after the mechanical breach, the impact would be significant in terms of lost growth of juveniles prior to entering the ocean and increased mortality rate at the smaller size. From a typical lagoon maximum WSE of 13 feet (NAVD88) prior to the mechanical breach down to a conservatively high minimum estuary WSE of 5.74 feet (NAVD88) would reduce lagoon volume from 472 to 24 acre feet (95% reduction); reduce area from 124 to 13 acres (90% reduction); reduce area with greater than 3 feet depth (preferred by steelhead) from 71 to 2.3 acres (96.5% reduction) (Whitson 2013).

Mechanical sandbar closure after the initial sandbar breach may re-establish lagoon depth and habitat value for steelhead remaining in the estuary after the initial breach. However, if excessive kelp and seagrass wash into the estuary between initial breach and subsequent closure, decomposition of this plant material in the lagoon may result in high BOD and water quality deterioration. This may create worse conditions than if the sandbar remained open. This scenario played out in Soquel Lagoon after the first October 1991 stormflow opened the barrier beach to the ocean. The opening was followed by 2 months without rain. Nearshore kelp and seagrass became trapped in the lagoon after the sandbar re-established, followed by decomposition for the next 2 months until storms resumed after Christmas (Alley 1992). A large, nearly anoxic zone (oxygen concentration less than 1 mg/l), likely uninhabitable by fish, existed for at least ½ mile of the lower lagoon.

The spring estuary provides rearing habitat for steelhead after their smolt migration from March to early June and primarily in April and May. Growth is rapid in the estuary with residence time in other Central Coast estuaries detected to be 2-3 weeks or more before entering the ocean. Water quality data indicate that oxygen and temperature conditions are good in Carmel Estuary except on limited occasions Fishery Analysis for The Carmel River-Lagoon Biological Assessment Report – January 2014 D.W. ALLEY & Associates Page 10

(MPWMD 2009-2013). However, if mechanical breaches occur during this period, substantial rearing habitat may be lost. In 4 of 20 years through WY2012, estimated mechanical breaches through the rainy season after the initial breach ranged from 4 to 8 times (Balance Hydrologics 2013). These breaching episodes resulted in periodic loss of good estuarine steelhead habitat, similar to the loss from the initial mechanical breach of the season, if they occurred in the April−May period of smolt rearing. If the estuary outlet channel is mechanically closed for the season before the smolt out-migration to the ocean is complete, a portion of the smolt population become trapped in the summer lagoon. Available data on water quality and lagoon depths indicate that mortality rate of these residualized smolts may be significant, with potential habitat of 1 meter or greater depth and adequate water quality becoming precariously limited late in the dry season of drier years, especially when tidal overwash and warm air temperatures occur in combination in the fall. Limited water surface temperatures collected in the south arm during drier years of 2004 and 2007 also indicated likely stressful water temperature throughout the lagoon during the months of July−September (MPWMD 2004−2008).

Water quality data summarized from the 2005 Carmel Lagoon (Lumas 2006) illustrated adequate steelhead conditions. However, salinity stratification and associated reduced water quality at depth likely forced steelhead nearer to the surface, making them more vulnerable to predation. Either depressed oxygen concentration to near 5 mg/l or less and/or elevated water temperature above 20°C were detected below 1 meter depth in the relatively deep south arm on a regular basis and in the main lagoon. Based on limited data, in dry years, such as WY2013 (MPWMD 2013), water quality conditions may deteriorate to the point that water temperature may exceed steelhead tolerance and water depth shallows to restrict habitat with at least 1 meter to primarily the south arm.

Steelhead mortality may occur from critically high water temperature after tidal overwash, especially when combined with persistent, warm air temperatures. The limited water quality data and observations at Carmel lagoon do not indicate lethal water quality conditions developing for steelhead in the fall after tidal overwash events and lack of stream inflow. However, lethal conditions may develop in the future under these conditions. Substantial steelhead mortality was observed in San Simeon Lagoon further south along the Central Coast in October 1995 under this scenario (Alley 1997b). Mortality was likely caused by salinity stratification after tidal overwash, high lagoon water temperature and low morning oxygen concentrations, with very low stream inflow and high air temperatures from Santa Ana-type winds.

Benefits of a Natural Breaching Regime It is likely that a northerly directed outlet channel will develop during the rainy season if unmanaged. According to Moffat and Nichol (2013), an elongated channel forms to the north along the beach in half of the years of observation (James, 2005) and either natural breaching or channel migration is expected to tend towards the northern alignment (Thornton, 2005). The lower berm elevations, due to milder beach slope and finer sediment, also favor natural breaching or channel migration towards the northern portion of the beach; however, this varies greatly on a year to year basis and depends on wave energy arriving over the winter/spring seasons. It has been observed that if the outlet channel first begins to migrate either north or south during the rainy season, it is likely to continue to migrate in that direction to the end of the rainy season (Hampson pers. comm. 2013). According to Moffat and Nichols (2013), local fisheries groups and agencies have preferred a northern meandering outlet channel alignment because, in the past,

Fishery Analysis for The Carmel River-Lagoon Biological Assessment Report – January 2014 D.W. ALLEY & Associates Page 11 when the river channel migrated northwards, it reduced the rate and amount of drawdown (drop in lagoon water levels before and after a breach to the ocean) and subsequent loss of threatened juvenile steelhead that get flushed out to sea, as compared to when the channel flows along the southerly and westerly outlet channel (James, 2005).

An extended lagoon phase (closed sandbar) in the fall provides a longer period of rapid juvenile steelhead growth and larger size and increased survival upon entering the ocean when the lagoon is largely evacuated. If the initial stormflow that threatens flooding is small and does not increase on succeeding days, the mechanical breach comes days to weeks earlier than an expected natural breach at the assumed 15 feet (NAVD88) low point elevation of the sandbar crest (Balance Hydrologics 2013). The natural breach would be expected 5 days or later after the initial mechanical breach in 5 of 20 years (25%) through WY2012 and would be expected 2−3 weeks later in 3 of the years (Refer to tables below; Balance Hydrologics 2013). Growth rate of juvenile steelhead in the closed Carmel Lagoon in October and November may be rapid. Data collected from Scott Lagoon in October and November 2005 indicated that juvenile steelhead grew at a rapid rate between 6.3 and 8.8 mm/week, on average (Beck et al. 2006). This extended lagoon habitat phase provided in 25% of the years by a natural breach instead of a mechanical breach would significantly increase juvenile steelhead size and survival rate upon entering the ocean from an evacuated estuary. Not all juveniles would be expected to enter the ocean, with some moving upstream into the river. However, some would. The juveniles that would move upstream would do so at a larger size, as well, to increase survival rate.

This extended growth phase from a natural breach would occur when the first stormflow of the season was small. In the 5 years when these delayed natural breaches were estimated to be 5 days or longer after the initial mechanical sandbar breach, stormflow at the time of mechanical breach was 18 cfs (2012), 19 cfs (2011), 29 cfs (2007), 21 cfs (1999) and 36 cfs (1996) (Refer to tables below; Balance Hydrologics 2013). Refer to the graphed streamflows at initial breachings below. Mechanical breaches at these low streamflows may attract adult steelhead into the estuary without sufficient streamflow for them to migrate further upstream or enough for them to migrate a limited distance upstream and become stranded until higher stormflow occurs. However, if the initial stormflows were higher or stormflow increased with succeeding days after the mechanical breach, the mechanical breach occurred just prior to when a natural breach would have been expected. According to James (2005), stream inflows greater than 100 cfs maintain an open estuary nearly all of the time because river flows sufficiently scour out beach sand. If the beach berm does close, it will fill in a day or two until it is either mechanically breached or naturally spills over the low point in the beach berm and breaches. Recorded data and field observations indicate that estuary inflows of more than 100 cfs will maintain an open estuary 95-100% of the time. Inflows of 20 cfs maintain an open estuary about 50% of the time, and the mouth will normally close at 10 cfs inflow or less. With wave action and reduced outflow after the stormflow subsides, the outlet channel begins to migrate often to the north and the minimum estuary WSE increases with a longer, lower gradient outlet channel. This provides deeper, more valuable steelhead habitat.

Steelhead Occurrences in the Project Area The South-Central California Coast steelhead DPS spawn and juveniles rear within the Carmel River. Population declines of steelhead along the west coast occurred due to widespread freshwater habitat degradation, simplification, and fragmentation from activities such as timber harvest, road construction, Fishery Analysis for The Carmel River-Lagoon Biological Assessment Report – January 2014 D.W. ALLEY & Associates Page 12 agriculture, ranching and mining activities, urbanization, as well as from water storage, withdrawal, conveyance, and diversions for irrigation, flood control, domestic, and hydropower purposes (NMFS 2006). The Carmel River historically supported a large steelhead run but that has declined by 90% or more (NMFS 2012b). Remaining estuarine habitat in the lagoon/wetlands is approximately 67% of historical habitat (NMFS 2012a). According to H.T. Harvey & Associates (2013), the south arm of the Carmel River Lagoon was enhanced in 1997-1998, and again in 2004 by deepening and extending the channel to increase habitat for steelhead and California red-legged frogs (Larson et al. 2006).

Adult Migration Adult steelhead migrate upstream from the ocean through an open sandbar and Carmel Estuary after prolonged storms, given the opportunity; the migration is primarily January –April but may start as early as late November and extend into May if late spring storms develop (MPWMD Fish Counter Data at San Clemente Dam for 2009−2013). With the median date for sandbar breaching of 29 December for 20 years of data (Balance Hydrologics 2013), adult migration has historically been delayed in the Carmel River until stormflow can overcome the depleted aquifer and dewatered conditions in the lower River to breach the sandbar. Many of the earliest migrants tend to be smaller than those entering the stream later in the season. Some adult steelhead may enter the estuary after relatively small storms and wait there until larger storms occur to allow upstream migration.

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Table 1. Carmel Lagoon First Seasonal Breach (FSB) of Each Year. Table 1. Carmel Lagoon first seasonal breach (FSB) of each year

Daily Mean Water Date of first Mechanical or Flow on day Date of assumed Year1 Wate Year Type2 breach3 Days into WY Natural4 of breach natural breach5 Days into WY (date) (days) (cfs) (date) (cfs) 2012 Dry 11/25/2011 56 Mechanical 18 12/16/2011 77 2011 Above Normal 11/24/2010 55 Mechanical 19 12/19/2010 80 2010 Above Normal 10/14/2009 14 Mechanical 759 10/14/2009 14 2009 Normal 2/16/2009 139 Mechanical 749 2/16/2009 139 2008 Normal 1/5/2008 97 Natural 509 1/5/2008 97 2007 Critically Dry 2/11/2007 134 Mechanical 29 2/16/2007 139 2006 Wet 12/28/2005 89 Mechanical 81 12/31/2006 92 2005 Wet 12/30/2004 91 Mechanical 532 12/30/2004 91 2004 Below Normal 12/30/2003 91 Mechanical 416 12/30/2003 91 2003 Normal 12/16/2002 77 Mechanical 1250 12/16/2002 77 2002 Below Normal 12/3/2001 64 Mechanical 402 12/3/2001 64 2001 Normal 1/11/2001 103 Mechanical 148 1/11/2001 103 2000 Above Normal 1/24/2000 116 Mechanical 1000 1/24/2000 116 1999 Normal 11/3/1998 34 Mechanical 21 11/23/1998 54 1998 Extremely Wet 12/6/1997 67 Mechanical 112 12/6/1997 67 1997 Above Normal 12/9/1996 70 Mechanical 27 12/10/1996 71 1996 Above Normal 12/13/1995 74 Mechanical 36 12/21/1995 82 1995 Extremely Wet 1/9/1995 101 Mechanical 445 1/9/1995 101 1994 Critically Dry 2/17/1994 140 Mechanical 106 2/18/1994 141 1993 Wet 1/3/1993 95 Mechanical 85 1/7/1993 99 Summary Statistics Average 85 337 90 Median 90 130 91 Maximum 140 1250 141 Minimum 14 18 14 Standard Deviation 33 367 30 Notes 1. Water Year (WY) is defined as October 1 of one year to September 30 of each subsequent year, for instance WY 2012 encompassed Oct 1, 2011 through September 30, 2012. 2. WY type as designated by MPWMD. 3. Date of first breach is defined as that in which the lagoon area > 2 feet in depth declines by > 20%. 4. The lagoon has been breached since the 1930's (CCoWS, Fall 2007), and in recent decades to prevent infrastructure flooding. 5. Date of assumed natural breach used an assumed seepage rate and known inflows that traced predicted changes in lagoon WSE and volume (Whitson Engineers, 2013b), and then to calculate date of assumed breach, using a WSE of 15 feet as the arbitrary elevation at which breaching would occur.

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Table 2. Carmel Lagoon Breaching Events and Days Open to Ocean. Table 2. Carmel Lagoon breaching events and days open to ocean Number of Number of natural mechanical Percent of time breaching breaching Wet season Wet season lagoon open to Water Year1 events3 events2 days open4 days closed5 the ocean6 (days) (days) (days) (days) (%) 2012 4 5 181 21 42 2011 0 5 247 12 62 2010 0 6 236 48 61 2009 2 1 109 5 24 2008 2 0 126 3 30 2007 3 1 58 17 6 2006 2 1 181 20 41 2005 0 1 199 2 53 2004 3 1 119 9 30 2003 1 1 206 1 54 2002 0 2 181 2 48 2001 0 1 153 0 39 2000 0 1 94 8 25 1999 0 8 205 38 54 1998 0 2 184 4 73 1997 0 1 160 0 42 1996 0 3 195 4 49 1995 0 1 211 0 55 1994 2 1 39 5 10 1993 1 1 175 2 47 Summary Statistics Average 1 2 163 10 42 Median 0 1 181 5 45 Maximum 4 8 247 48 73 Minimum 0 0 39 0 6 Standard Deviation 1 2 56 13 17 Notes 1. Water Year (WY) is defined as October 1 of one year to September 30 of each subsequent year, for instance WY 2012 encompassed Oct 1, 2011 through September 30, 2012. 2. Mechanical breaching events were counted as (a) first breach of the year unless reported otherwise, and (b) when reports indicated additional mechanical breaches. 3. Natural breaching events were counted when lagoon closures were (a) on the order of 1-2 days and (b) when flows were > 50 cfs 4. Wet season days open is defined as number of days from first breach to final closure, not counting wet season days closed. 5. Wet season days closed is defined as those days when WSE remained > 11 feet (NAVD88) for longer than 24 hours. 6. Percent of time WY lagoon open to the ocean is defined as wet season days open minus wet season days closed divided by 365 days per year times 100.

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Chart 1. Carmel River Mean Daily Flow at First Mechanical Breach of Sandbar Barrier, 1993─2012. Data from Balance Hydrologics Technical Memorandum (2013).

Carmel River Mean Daily Flow at First Mechanical Breach of Sandbar Barrier, 1993─2012. Data from Balance Hydrologics Technical Memorandum (2013). 1300

1200

1100

1000 Mean Daily Flow at First Mechanical Breach (Natural Breach in 2008)

900

800

700

600

500

Mean Daily Flow (cfs) FlowDaily Mean 400

300

200

100

0

1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 Water Year

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Spawning Steelhead require spawning sites with gravels (from 1/4" to 3 1/2" diameter) having a minimum of fine material (sand and silt) and with good flows of clean water moving over and through them. Flow of oxygenated water through the redd (nest) to the fertilized eggs is restricted by increased fine materials from sedimentation and cementing of the gravels with fine materials. Flushing of metabolic wastes is also hindered. These restrictions reduce hatching success. In many local streams, steelhead appear to successfully utilize spawning substrates with high percentages of coarse sand, which probably reduces hatching success. Spawning habitat in the Carmel River, downstream of San Clemente Dam, is limited and relatively low quality compared to upstream due to low gradient geomorphology leading to limited spawning glides, limited spawning gravel and a high proportion of fine sediment (Alley 1991). The highest quality spawning habitat exists upstream of Los Padres Dam (Alley 1990; 1995a).

Steelhead spawning success may be limited by scour from winter storms. Steelhead that spawn earlier in the winter are more likely to have their redds washed out or buried by the greater number of winter and spring storms that will follow. Young-of-the-year (YOY) steelhead production is related to spawning success, which is a function of the spawning habitat quality, the pattern of storm events and ease of spawning access to upper reaches of tributaries, where spawning conditions are generally better.

After spawning, eggs incubate in the gravel for 3 weeks to 2 months prior to hatching (quicker at higher temperatures), and fry emerge 2-6 weeks post-hatch in spring or early summer (NMFS 2007). Once fry emerge from the gravels, they may remain near their natal areas or migrate downstream to other areas for rearing. A portion of the young that emerge from their redds closest to the lagoon will migrate to the lagoon to rear. Most juveniles spend 1-2 years (growing seasons), depending on growth rate, in the Carmel River and other Central Coast watersheds before smolting and entering the ocean, (Alley 2013b).

Summer Rearing Young-of-the-year steelhead enter the lagoon/estuary in June and July, inhabiting the summer/fall lagoon to grow rapidly in very productive nursery habitat (Alley and Smith 1987-88 trapping data; Alley 1997; Alley 2013a). Juvenile steelhead that rear in the productive Carmel Lagoon require only one growing season to reach smolt size (Alley 1997a). Juvenile steelhead have been captured by seining in the mouth of the north and south arms by MPWMD staff in multiple past years, indicating they use these areas for rearing when they are accessible (Kevan Urquhart, personal communication). According to H.T. Harvey & Associates (2013), a large school of juvenile steelhead was detected in underwater video surveys conducted in the north arm in July 2006 (Larson et al. 2006). Dettman observed large groups of juvenile steelhead in the deep south arm between the pipeline crossing and the main lagoon during past summer snorkeling activities (David Dettman, pers. comm. 2011). According to H.T. Harvey & Associates (2013), fish were reported in the deeper waters of the south arm of the Carmel River Lagoon from sonar surveys in the fall of 2007 and 2008; in 2007, most of the fish were likely steelhead, but in 2008 they may have been steelhead or bass or both (CSUMB Class 2008). However, Caspian terns and pelicans were observed preying heavily upon juvenile steelhead when steelhead were forced into the upper portions of the water column in a salinity-stratified Carmel Lagoon (Dettman 1984), where the bottom saline layer becomes stagnant, warm and low in oxygen concentration when the sandbar is closed. This indicated high predator vulnerability when juveniles cannot, or choose not to, utilize greater depths.

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Steelhead sampling in October 1996 (Alley 1997) in Carmel Lagoon (prior to deepening of the south arm) indicated that steelhead congregated in the deepest portion of the main lagoon, which was along the southern margin of the main embayment, having cattails along the margin, east of the mouth of the south arm and at depths of 1 to 1.5 meters. Steelhead observations and capture data indicated that deeper estuarine/lagoon habitat is better for steelhead rearing than shallow habitat, especially when lagoon conditions are unstratified in terms of salinity and water temperature, and when estuarine conditions remain mixed and cool with daily tidal influences. The 1996 Carmel Lagoon steelhead population estimate, based on mark and recapture, was 5,643 with a standard error +/-551. A total of 565 juveniles were marked on 7 October and 81 were recaptured of the 809 captured on 13 October. The median size of 216 juvenile steelhead measured on 7 October was 125-129 mm Standard Length. This was within the range of juvenile steelhead sizes captured in Soquel Creek over the past 16 years (105-110 mm SL to 155- 159 mm SL; Alley 2013a), indicating that juvenile growth rate was rapid in Carmel Lagoon.

The Carmel Lagoon WSE had increased more than 2 feet in the week between samplings in October 1996, due to tidal overwash. Stream inflow to the lagoon had continued throughout the dry period in 1996 but diminished to less than 0.2 cfs. The lagoon WSE was estimated at approximately 6.40 ft (NAVD88) on 7 October prior to tidal overwash, based on WSE tracings for WY1997 (Balance Hydrologics 2013). It was measured at 8.15 ft (NAVD88) on 16 October and estimated to be similar to 13 October (Alley 1997a). Sizeable tidal overwash on 8 October had raised the lagoon WSE to an estimated 9.15 ft based on WSE tracings for WY1997 (Balance Hydrologics 2013). The lowest WSE that summer was approximately 5.49 ft (NAVD88) on 28 August (Alley 1997a). Surface water temperature was 22°C at 1720 hr on 7 October before tidal overwash. Surface water temperature was 19°C at 1253 hr on 13 October after tidal overwash and 18°C at 1214 hr on 16 October (air temperature 18°C at 1353 hr) on a windy day without stratification of temperature (17.5−18.2°C through the upper meter of depth in mid- afternoon) or salinity (17-18 ppt through the upper meter of depth) and fair to good oxygen concentrations (between 5 and 8 mg/l through the upper meter at 9:00 am−12:00 pm). However, stratification and oxygen depletion occurred in the deep South Arm below 1.5 m from the surface. The steelhead presence in high numbers in October 1996 indicated that the lagoon provided valuable summer rearing habitat when stream inflow to the lagoon continued throughout the summer/fall. The two samplings of steelhead and water quality measurements taken before and after sizeable tidal overwash indicated that conditions were tolerable for steelhead under windy conditions that encouraged water column mixing and under relatively cool air temperatures.

Smolt Migration Pre-smolts and smolts (young steelhead which have physiologically transformed in preparation for ocean life) migrate downstream to the Carmel Estuary in March to May and on into the Monterey Bay. The heaviest migration to the estuary is from mid-March through mid-May, based on smolt trapping data (MPWMD 1999, 2007 and 2013). However, WY2007 and 2013 were critically dry, with smolt migration expected to be earlier than wetter years having more stormflow and higher turbidity. Turbidity reduces feeding efficiency and growth rate. It should be noted that smolts trapped at the various locations had yet to reach the estuary, and in the case of those trapped below Los Padres they had another 20+ miles of passive migration to reach the estuary. Also, with 2-3 weeks of residence time in the estuary by would-be smolts to increase in size prior to entering the ocean, actual emigration to the ocean may not occur until late May for many smolts. Smolt trapping in the San Lorenzo River just above the estuary during dry Fishery Analysis for The Carmel River-Lagoon Biological Assessment Report – January 2014 D.W. ALLEY & Associates Page 18 years indicated smolt migration extending well into May (Smith and Alley data 1987−88). On some trapping nights, a majority of the down-migrants were pre-smolts with partial smolt coloration. These pre- smolts may spend weeks in the estuary to complete the smolt transformation and grow larger before entering the ocean (Smith unpublished data from Waddell Creek smolt trapping/ marking (1992-1995) and subsequent estuary sampling). As juveniles reach the estuary, the larger individuals are ready to enter the ocean directly. However, others have not completed the smoltification process. According to Dr. Carl Schreck, fish physiologist at Oregon State University (pers. comm. 2010), the smoltification process can be completed without prior exposure to saltwater. Fully smolted juvenile steelhead can go directly from freshwater to saltwater without any problem and without prior exposure to brackish water. However, Dr. Schreck stated that the rate of smolting is variable among fish and that brackish water will facilitate the completion of smoltification in some fish. Research has shown that gradual adaptation to salt water of increasing salinities results in much greater smolt survival than direct entry into full strength seawater, especially when fish show minimal smolt development (NOAA Tech Memo NWFSC-7 1993).

Down-migrant juveniles may spend variable time in the estuary and may grow considerably while there, increasing their probability of returning as adults. Dr. Smith (pers. comm. 2013) reported that pre-smolts trapped at 100 mm Standard Length in Waddell Creek in late April were recaptured in Waddell Estuary 2- 3 weeks later in early-mid May at 125-140 mm SL with full smolt coloration. Smith added that smolts may grow 50 mm in a few weeks as occurred in San Gregorio Estuary (Atkinson 2010). Smith’s and Atikinson’s findings indicate the importance of allowing at least a 2-3 week estuary residence time for smolts in May to grow considerably prior to entering the ocean. Ocean survival to adulthood is positively correlated with increased smolt size (Shapovalov and Taft 1954; Bond 2006; Bond et al. 2008). Dettman observed large groups of steelhead smolts in the south arm between the pipeline crossing and the main estuary during past spring snorkeling activities (David Dettman, per. comm. 2011). The south arm is typically a deeper portion of the estuary. Atkinson (2010) found larger smolts in San Gregorio Estuary in April 2008 that stayed longer in the estuary with associated higher growth rate and size than smolts captured in April 2006, after a wetter winter and higher spring runoff. Atkinson concluded that the partially impounded salinity-stratified San Gregorio estuary in April 2008 was much more productive than in April 2006, when it was shallow, unstratified and completely fresh. Steelhead observations and capture data indicate that deeper estuarine habitat is better for rearing of pre-smolts and smolts than shallow habitat, especially when estuarine conditions remain mixed and cool with daily tidal influences. Atkinson’s findings indicate that the deeper, somewhat stratified 2008 San Gregorio estuary provided sufficiently mixed conditions that were adequately cool and were sufficiently oxygenated to create adequate oligohaline estuarine habitat to rear fast-growing steelhead smolts. These conditions would be beneficial for smolts in the Carmel Estuary prior to entering the ocean.

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Chart 2. Actual Daily and Cumulative Smolt Catch Over Time Below Los Padres Dam, 1999.

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Chart 3. MPWMD Steelhead Smolt Trapping – Scarlett Site, 2007.

Chart 4. MPWMD Steelhead Smolt Trapping – Scarlett Site, 2013.

(Water Years 2007 and 2013 were critically dry, leading to earlier smolt migration than wetter years because of higher water clarity, feeding efficiency and growth rate in spring.) Fishery Analysis for The Carmel River-Lagoon Biological Assessment Report – January 2014 D.W. ALLEY & Associates Page 21

Chart 5. San Lorenzo River Smolt Trapping, 1987.

San Lorenzo River Smolt Trapping Above Estuary, 1987, a Dry Year. (Smith, Alley and Lehr Data)

150 140 Steelhead Smolts 130 120 Steelhead YOY 110 100 90 80 70 60 50 40 30 20 10 0

Jun Jun Number of Juvenile of Juvenile NumberSteelheadTrap / Night Apr Apr - - Mar - - May May - - - 6 9 20 11 25 28 23 Date

Chart 6. San Lorenzo River Smolt Trapping, 1988.

San Lorenzo River Smolt Trapping Above Estuary, 1988, a Dry Year. (Smith, Alley and Lehr Data) 140 130

120 Steelhead Smolts 110 Steelhead YOY 100 90 80 70 60 50 40 30

Number of SteelheadNumber / Trap Night 20 10 0

Jun Jun Apr Apr Apr Apr - - Mar - - - - May May May - - - - 5 9 7 18 16 23 30 27 15 21 Date

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Table 3. Historical Record of Natural Sandbar Closure at Santa Rosa Lagoon (1993–2007) with Groundwater Wells Influencing Streamflow in Drier Years (from Alley 2008).

Year Date of First Sandbar Sampling evidence Stream Inflow Closure Detection After of Smolts in the Cubic feet/ second (cfs) Winter/Spring Rainy Lagoon or Season Immediately Upstream After Sandbar Closure 1993 24 May 1993 closed (Re- Yes (few) 7.9 cfs on 24 May opened after light rain 4.15 cfs on 11 June on 25 May 1993) 11 June 1993 (or sooner) 1994 28 March 1994 Yes (many) 2.49 cfs on 29 April

1995 28 May 1995 Yes (few upstream No data. only) 1996 3 June 1996 Yes (very few 5.13 cfs on 29 May upstream only) 2.98 cfs on 12 June 1997 23 March 1997 Yes (many) 12.60 cfs on 26 Mar

1998 13 July 1998 Yes (very few 4.65 cfs on 15 July upstream only) 1999 28 May 1999 No (upstream not 6.18 cfs on 28 May sampled) 2000 31 May 2000 No (upstream not 3.00 cfs on 15 June sampled) 2001 14 May 2001 No (upstream not 4.40 cfs on 23 May sampled) 2002 14 April 2002 Yes (many) 2.14 cfs on 28 Feb. 2.11 cfs on 28 Mar. 1.13 cfs on 29 April 2003 9 June 2003 No 1.50 cfs on 3 July

2004 7 May 2004 Yes (few upstream 2.69 cfs on 21 May only) 2005 27 May 2005 Yes (few upstream 6.25 cfs on 16 June only) 2006 Sometime between 24 No 18.67 cfs on 24 May May and 26 June 2006 3.23 cfs on 12 July 2007 15 March 2007 Yes (many) 21.94 cfs on 1 Mar.

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Physical and Biological Aspects of the Carmel Lagoon/Estuary Pertaining to Steelhead Habitat and Rational for Assessing Impacts of Proposed Actions

Food Web In a stable estuary, the central embayment has periodic, small tidal influxes of kelp and seagrass that become decomposing detrital material in slackwater habitats. This plant detritus can support abundant invertebrates (may fly larvae, Chironomus (black fly larvae), water boatmen, Physa snails, mollusks, isopods, Neomysis shrimp, Eogammurus, and amphipods, such as Corophium) as potential fish food (Alley et al. 1990; Alley 1992). Most of these are euryhaline (salinity-tolerant) except for Chironomus, and thrive in estuaries and freshwater lagoons when oxygen levels are good and plant life is abundant. Macroinvertebrate work done in the Central Coast Pescadero Estuary/Lagoon indicated that marine and euryhaline species were abundant in spring and early summer when the stream mouth was open and salinity ad dissolved oxygen levels were high and marine macroalgae were abundant (Robinson 1993). When the stream mouth became closed by sandbar formation, saltwater was trapped in the lagoon and the water column became stratified. Saline dewater areas became warm and hypoxic or anoxic. As a result, marine species disappeared and euryhaline species declined with hypoxic/anoxic conditions, reduced salinities and decreases in phytoplankton and macro algae as food. However, by September pondweed had increased and the lagoon had converted to a destratified freshwater lagoon. At this time the euryhaline and freshwater macroinvertebrate species increased and were positively correlated with dissolved oxygen and pondweed abundance. The nutrients contributed from detrital decomposition stimulate phyto-planktonic algal blooms that support abundant Neomysis shrimp. These invertebrates can be consumed by fast-growing, down-migrant steelhead before they enter the ocean. These perspective smolts may grow 1-2 inches, or more, during their stay in the spring estuary (Jerry Smith, pers. comm. 2013), greatly increasing their survival rate in the ocean. More estuarine steelhead habitat exists when greater residual pool volume exists at low tide. When the outlet channel is allowed to meander diagonally and laterally creating a long outlet channel across the sandbar (either south or north), greater estuary depth and extent is protected. These lateral outlet channels result in a decrease in both the rate of lagoon draw-down, and a reduction in the total drop in lagoon level. Smaller stormflows are directed laterally through the sandbar under these conditions, resulting in generally slower draining and less sandbar erosion. The result of these lateral outlet pathways is higher retention of estuary pool volume and greater residual estuary depth and steelhead habitat after stormflow recedes.

Water Temperature Juvenile steelhead may inhabit the lagoon and estuary year round, though their critical use for growth is in spring for pre-smolts and summer-fall for juvenile growth. They have physical tolerances for water temperature and oxygen concentrations, and become acclimated to salinity and higher water temperatures. The lethal level for steelhead would probably be above 26-28ºC (79-82ºF) for several hours during the day. But this is rarely, if ever reached. Even so, warmer temperatures could result in slower growth or starvation in steelhead if food supply becomes very limited. Sub-lethal effects of high temperatures on salmonids include increased metabolic rates and decreased scope for activity, decreased food utilization and growth rates, reduced resistance to disease and parasites, increased sensitivity to some toxic materials, interference with migration, reduced ability to compete with more temperature resistant species and reduced ability to avoid predation. At sub-lethal levels water temperature is largely a food availability issue. If food is scarce, low temperatures (10-14ºC or less) would be optimal, because they reduce basal

Fishery Analysis for The Carmel River-Lagoon Biological Assessment Report – January 2014 D.W. ALLEY & Associates Page 24 metabolic rate, reducing food needs and resulting in lower summer weight loss (if food is very scarce). If food is moderately abundant higher temperatures (14-18ºC) would be optimal, because metabolic rate would not be too high, and swimming performance and digestive rate would allow for active feeding and growth. If food is very abundant and available, then warmer temperatures (18-22ºC) might be optimal, because rapid digestion would allow fish to quickly assimilate the abundant food and growth rate would be high.

Kubicek and Price (1976) concluded that although temperatures less than 26.5ºC (79.7ºF) were not assumed to directly cause steelhead mortality in the Big Sulphur Creek drainage (tributary to the Russian River, Mendocino County), temperatures consistently above 20ºC (68ºF) were assumed to cause sub- lethal stress that could result in decreased fish production and indirect mortality. They noted that juvenile steelhead disappeared from a section of Big Sulphur Creek when hot springs caused summer temperatures to rise above 26ºC. They assumed in their monitoring that stations that had temperatures greater than 20ºC (68ºF) for less than 50% of the time in any one month were not expected to cause significant sub- lethal effects in that month, unless that station reached a marginal or lethal maximum temperature.

Charlon (1970) found that steelhead acclimated at 24ºC (75.2ºF) experienced a lethal temperature of 26.35ºC (79.4ºF). Alabaster (1962) found steelhead acclimated to 20ºC (68ºF) to experience a lethal temperature of 26.6ºC. McAfee (1966) found steelhead lethal temperatures in the range of 24-29ºC (75.2º- 84.2ºF) with unspecified acclimation temperatures.

There are many central coast examples of steelhead surviving and growing well at water temperatures above 21ºC. Many of these come from coastal lagoons (Alley 2002a) and lower reaches of unshaded drainages, such as lower Soquel Creek (Alley 2002b) and the lower San Lorenzo River (Alley 2001c), but only where food is abundant. When food is abundant, growth is actually better at warmer temperatures because digestive rate is increased, allowing fish to consume more food and grow more quickly.

Oxygen Levels Steelhead have been observed at oxygen levels below 4 mg/l in many locations along the central coast. Steelhead were captured from isolated pools (stream discontinuous) at 3-4 mg/l oxygen and 16º C water temperature in 1988 in Waddell and Redwood creeks in Santa Cruz and Marin counties, respectively (J. Smith, pers. comm. 1998), but coho were absent from the pools in Redwood Creek where levels dropped to 3 mg/l. In August 1989 on the Carmel River, juvenile steelhead were observed in pools at three different sites where oxygen ranged from a minimum of 2-4 mg/l at the different sites before dawn to a maximum of 14-15.5 mg/l (super saturation) in the afternoon, with water temperature ranging from 61º F (16.1º C) in the morning to 72º F (22.2º C) in late afternoon (D. Dettman, pers. comm. 1993).

In San Simeon Creek Lagoon in 1993, steelhead survived to at least mid-August, despite morning oxygen levels in the 1.7-2.8 mg/l range. Juvenile steelhead were observed on 10 June, and 29 July at the same location (Alley, pers. observation 1993). On 11 June the maximum oxygen concentration at that station was 2.7 mg/l at 0603hr (at the surface), with water being 14º C (Alley 1995b). On 8 July the maximum oxygen level was 1.7 mg/l with water at 16º C at 0525 hr (Alley 1995b). On 29 July the oxygen concentration was at a maximum of 2.8 mg/l with water temperature of 17.5º C at 0530 hr (Alley 1995b).

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An adult steelhead was observed in the lagoon during sampling on 10-11 August (J. Nelson, California Department of Fish and Game, pers. comm. 1993).

At low temperatures, it was reported that rainbow trout withstand oxygen concentrations of 1.5 to 2 mg/l (Moyle 1976). Rainbow trout were found in Penitencia Creek (Santa Clara County) at 3 mg/l oxygen and 20º C water temperature (J. Smith personal comm. 2003).

Discussion of Critical Environmental Factors Though steelhead may tolerate, for short periods, water temperature above 26 C at the end of the day and oxygen concentrations below 2 mg/l for a couple of hours at dawn, they do best in lagoons when morning water temperatures are 20 C or less (unlikely to increase more than 3 C through the day) and oxygen concentrations are above 5 mg/l (likely to increase through the day from photosynthesizing aquatic vegetation). Oxygen concentration is typically lowest at dawn and may remain low through the morning if heavy fog is present. It increases through the day from photosynthesis of algae and other submerged vegetation, such as pondweed. Increased salinity associated with tidal overwash appear to reduce their high temperature and low oxygen tolerances. Water depth of 1 meter (approximately 3 feet) or deeper is preferred by steelhead in the open water lagoon/estuary based on personal observations. Vulnerability to bird predation increases as water depth decreases.

Physical conditions and aquatic habitat change seasonally in the lagoon and estuary. A closed barrier beach develops at the Carmel rivermouth at end of the rainy season with a closed lagoon established. During the last 3 years (2011−2013), the lagoon has been mechanically closed to maximize the initial lagoon WSE. Lagoon WSE declines through the summer as stream inflow declines below the seepage rate through the sandbar and evaporation occurs. Seepage through the sandbar transports heavier saltwater through the bar, and the summer lagoon becomes less saline to the point where saltwater remains only in the deeper south arm. Lack of saltwater stratification throughout most of the lagoon will result in a cooler lagoon. Freshwater throughout the water column promotes daily turnover of lagoon water from wind, which cools water exposed to cooler nightly air temperatures. The stagnant saltwater lens at depth in the south arm increases water temperature and decreases in oxygen concentration relative to the upper freshwater layer that mixes with the air (Alley 1997a; MPWMD 2009-2013). Steelhead avoid excessively high water temperature and low oxygen found at greater water depth where saltwater is present. Habitat with the coolest temperature and highest oxygen concentration under the deepest conditions have the highest habitat value for steelhead. Habitat value increases if there is a peripheral tule bed associated with these conditions to provide good escape cover. Unless feeding, steelhead typically stay at least 1 meter from the surface or just off the bottom in shallower locations.

Inspection of lagoon/estuary water quality data collected through the water column by the MPWMD in 2009-2012 indicated adequate water quality for juvenile steelhead except on limited occasions. Data were limited in summer/fall 2009 to August and September and did not include October or November. Where water depth was greater than 1 meter, data were assessed at 1 meter depth. Where water depth was less than 1 meter, data were assessed at the reading above the bottom, usually 0.25 meter above.

Water quality parameters included temperature, oxygen and salinity. Water quality measured in the morning was assessed, using the following table from our previous Soquel Lagoon water quality

Fishery Analysis for The Carmel River-Lagoon Biological Assessment Report – January 2014 D.W. ALLEY & Associates Page 26 assessments and was based on steelhead tolerances and expected increases in oxygen and water temperature through the day.

Table 4. Criteria for rating water quality measurements within 0.25 Meters of the bottom or at 1 meter if salinity stratification caused oxygen depletion at greater depth (from Alley 2013a).

Morning Water Morning Temperature Morning Oxygen Quality Rating (Celsius) (mg/L) Good <20 >7 Fair 20-21.5 5-7 Poor 21.5-23 2-5 Critical >23 <2

Oxygen concentrations often diminished while water temperature increased with depth when salinity stratification occurred after saltwater was retained when the sandbar closed for the dry season or after tidal overwash occurred into the closed lagoon, usually in the fall. However, adequate water temperature and oxygen levels for steelhead survival were present in the upper 1 meter of depth at stations in the main lagoon and the south arm for all data available for 1996, 2005, 2009─July 2013 except for late June 2013 in a critically dry year. Adequate water temperature and oxygen levels for steelhead existed in the north arm much of the time. That is to say, morning oxygen levels above 5 mg/l and morning water temperature 20°C or less occurred in the upper 1 meter depth of the lagoon/estuary at stations in nearly all months of all years for the periods of available water quality collected through the water column. However, WY 2013 was very dry, with the lagoon was mechanically closed for the season on April 10. By late June 2013, lagoon monitoring sites in the north arm, main embayment and the south arm had water temperatures between 24°C and 25°C measured between 1230 and 1400 hr, which were critically high for steelhead and were likely to increase through the day. Oxygen levels by early afternoon were good and above 10 mg/l in the upper 1 meter. Water depth was only 0.5 m deep at the main embayment station. The only station with more than 1 meter depth was in the south arm.

Limited water surface temperatures collected in the south arm during drier years of 2004 and 2007 also indicated likely stressful water temperature throughout the lagoon during the months of July−September (MPWMD 2004−2008). In both years, weekly, early afternoon water temperature measurements were above 22°C and reached 26.7°C at 1545 hr on 24 July 2004 in a below normal water year. Water temperatures likely increased 1−2°C by late afternoon on those days. These elevated water temperatures indicated stressful habitat conditions for steelhead.

Water quality data summarized from 2005 (Lumas 2006) illustrated adequate steelhead conditions (Charts 7-12). However, salinity stratification and associated reduced water quality at depth likely forced steelhead nearer to the surface, making them more vulnerable to predation. Caspian terns and pelicans have been observed preying heavily upon juvenile steelhead that had been forced into the upper water column in the salinity-stratified Carmel Lagoon (Dettman 1984). Either depressed oxygen concentration to near 5 mg/l or less and/or elevated water temperature above 20°C were detected below 1 meter depth in the relatively deep south arm on a regular basis and in the main lagoon in late July 2010, early September 2010, early October 2010, early November 2010, early July 2011, late September 2011, late October 2011, late November 2011 (after mechanical opening of sandbar and subsequent mechanical closure), late Fishery Analysis for The Carmel River-Lagoon Biological Assessment Report – January 2014 D.W. ALLEY & Associates Page 27

June 2012, late September 2012 and late October 2012. In mid-October 1996 after tidal overwash, oxygen levels below 5 mg/l and/or water temperature above 20°C were not detected in the upper 1 meter of the central embayment but at peripheral stations in the north arm and upper main lagoon, as well as in the south arm (Alley 1997a). Water quality in mid-November 1996 was improved at all stations. Based on limited data, in dry years, such as WY2013, water quality conditions may deteriorate to the point that water temperature may exceed steelhead tolerance and water depth shallows to restrict habitat with at least 1 meter to primarily the south arm.

The limited water quality data and observations at Carmel lagoon do not indicate lethal water quality conditions developing for steelhead in the fall after tidal overwash events and lack of stream inflow. However, lethal conditions and significant steelhead mortality (295+ juvenile steelhead) were observed in

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Chart 7. Morning Oxygen Levels and Gage Heights in the Central Embayment of the Carmel Lagoon/Estuary, 2005.

Morning Oxygen Levels (Within 0.25 m of Bottom or at 1 meter if Depth Exceeded 1 meter) and Gage Heights in Central Embayment of the Carmel Lagoon/Estuary, 2005. (Data from Lumas 2006)

20

18 R1N- Oxygen

16 R2- Oxygen

Gage Ht (NAVD88) 14

12

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8

6 Oxygen Oxygen (mg/L andGage Height (ft)

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0 Jul Jul Jul Jul - - - - Oct Oct Oct Oct Oct Sep Sep Sep Sep Dec Dec Dec Dec Dec Aug Aug Aug Aug Nov Nov Nov Nov ------9 ------1 8 3 3 16 23 30 6 5 15 22 29 10 17 24 10 17 24 31 13 20 27 12 19 26 Date

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Chart 8. Morning Oxygen Levels and Gage Heights in the South Arm of the Carmel Lagoon/Estuary, 2005.

Morning Oxygen Levels (Within 0.25 m of Bottom or at 1 meter if Depth Exceeded 1 meter) and Gage Heights in South Arm of the Carmel Lagoon/Estuary, 2005. (Data from Lumas 2006) 20

18 SH1 North- Oxygen

16 S2 South- Oxygen

14 Gage Ht (NAVD88)

12

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6 Oxygen Oxygen (mg/L) andGage Height (ft)

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0 Jul Jul Jul Jul - - - - Oct Oct Oct Oct Oct Sep Sep Sep Sep Dec Dec Dec Dec Dec Aug Aug Aug Aug Nov Nov Nov Nov ------9 ------1 8 3 3 16 23 30 6 5 15 22 29 10 17 24 10 17 24 31 13 20 27 12 19 26 Date

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Chart 9. Morning Oxygen Levels and Gage Heights in the North Arm of the Carmel Lagoon/Estuary, 2005.

Morning Oxygen Levels (Within 0.25 m of Bottom or at 1 meter if Depth Exceeded 1 meter) and Gage Heights in North Arm of the Carmel Lagoon/Estuary, 2005. (Data from Lumas 2006) 16

N1 East- Oxygen 14 N2 West- Oxygen

Gage Ht (NAVD88) 12

10

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6 Oxygen (mg/L)Oxygen and Gage Height (ft) 4

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0 Jul Jul Jul Jul - - - - Oct Oct Oct Oct Oct Sep Sep Sep Sep Dec Dec Dec Dec Dec Aug Aug Aug Aug Nov Nov Nov Nov ------9 - - - - 1 8 3 3 6 16 23 30 5 15 22 29 10 17 24 10 17 24 31 13 20 27 12 19 26 Date

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Chart 10. Morning Water Temperature and Gage Heights in the Central Embayment of the Carmel Lagoon/Estuary, 2005.

Morning Water Temperature (Within 0.25 m of Bottom or at 1 meter if Depth Exceeded 1 meter) and Gage Heights in Central Embayment of the Carmel Lagoon/Estuary, 2005. (Data from Lumas 2006) 24

22 R1N- Temp 20

R2- Temp 18 Gage Ht (NAVD88) 16

14 C) Gage and Height (ft)

° 12

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6 Water TemperatureWater (

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0 Jul Jul Jul Jul - - - - Oct Oct Oct Oct Oct Sep Sep Sep Sep Dec Dec Dec Dec Dec Aug Aug Aug Aug Nov Nov Nov Nov ------9 ------1 8 3 3 16 23 30 6 5 15 22 29 10 17 24 10 17 24 31 13 20 27 12 19 26 Date

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Chart 11. Morning Water Temperature and Gage Heights in the South Arm of the Carmel Lagoon/Estuary, 2005.

Morning Water Temperature (Within 0.25 m of Bottom or at 1 meter if Depth Exceeded 1 meter) and Gage Heights in South Arm of the Carmel Lagoon/Estuary, 2005. (Data from Lumas 2006) 26

24 SH1 North- Temp 22 S2 South- Temp

20 Gage Ht (NAVD88) 18

16

14 C) Gage and Height (ft) ° 12

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Water TemperatureWater ( 6

4

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0 Jul Jul Jul Jul - - - - Oct Oct Oct Oct Oct Sep Sep Sep Sep Dec Dec Dec Dec Dec Aug Aug Aug Aug Nov Nov Nov Nov ------9 - - - - 1 8 3 3 6 16 23 30 5 15 22 29 10 17 24 10 17 24 31 13 20 27 12 19 26 Date

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Chart 12. Morning Water Temperature and Gage Heights in the North Arm of the Carmel Lagoon/Estuary, 2005.

Morning Water Temperature (Within 0.25 m of Bottom or at 1 meter if Depth Exceeded 1 meter) and Gage Heights in the North Arm of the Carmel Lagoon/Estuary, 2005. (Data from Lumas 2006) 28

26 N1 East- Temp 24

22 N2 West- Temp

20 Gage Ht (NAVD88) 18

16 C) Gage and Height (ft)

° 14

12

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Water TemperatureWater ( 6

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0 Jul Jul Jul Jul - - - - Oct Oct Oct Oct Oct Sep Sep Sep Sep Dec Dec Dec Dec Dec Aug Aug Aug Aug Nov Nov Nov Nov ------9 ------1 8 3 3 16 23 30 6 5 15 22 29 10 17 24 10 17 24 31 13 20 27 12 19 26 Date

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San Simeon Lagoon further south along the Central Coast. It occurred 2-5 October 1995 after substantial tidal overwash on 27-29 September and 2 weeks of high lagoon salinity with a lower than usual sandbar crest (Alley 1997b). These conditions could also occur at Carmel Lagoon and are, therefore, relevant to the discussion. Mortality was likely caused by salinity stratification, high lagoon water temperature (22- 24°C) and low morning oxygen concentrations (2.8-4.2 mg/l on 2 October and less than 1.5 mg/l by 4 October) with very low stream inflow (0.13 cfs) and high air temperatures from Santa Ana-type winds (extremely dry down-slope winds that originate inland and affect coastal regions) (+32°C (+90°F)) for days without morning fog and thick filamentous algae present. Active pumping of well water into the lagoon during the period 4-13 October improved water quality and stopped the fish kill. The artificially high inflow of more than 1.5 cfs flushed the saltwater layer from the lagoon, cooled the lagoon and initially raised oxygen levels. By 10 October, morning oxygen levels were back down to 2 mg/l in the upper lagoon, but the morning fog pattern had re-established to maintain a cool lagoon. On 6 October 1995, dead steelhead were also observed in Little Pico Lagoon further north.

The lagoon shallows through the summer as stream inflow declines below the sandbar seepage rate, combined with evaporation rate. Summer streamflow is usually ephemeral as it goes subsurface in the Carmel River (except in the wettest years). Steelhead habitat deteriorates, with areas having 1 meter depth or more (which steelhead prefer in order to avoid predation) disappearing and water quality declining beyond steelhead tolerances. With shallow summer lagoon conditions, water temperature may become elevated and critically high for steelhead if air temperatures become elevated without incidence of morning fog and/or nightly cooling. In drier years, lagoon WSE is quite low in summer with shallow conditions 0.5 meters or less in much of the lagoon, except for the south arm and the main embayment on the south side. If air temperatures become high without morning fog and/or with persistently warm air temperatures through the night under these shallow conditions, water temperature may exceed 24°C by early afternoon, as occurred in June 2013 (MPWMD data).

Lagoon WSE, surface area, volume and depth increase in the fall after typical tidal overwash in October and November. This may cause further water quality deterioration from increased saltwater stratification, higher water temperatures and lower oxygen concentrations. The heavier saltwater becomes stratified along the lagoon bottom, collecting in the deep south arm initially and spreading into the main embayment as tidal overwash increases. Generally, the upper one meter of the lagoon is mostly freshwater, with water temperatures less than 20°C and oxygen levels above 5 mg/l. At greater depth where the saltwater lens stagnates, temperature often becomes elevated above 20°C and oxygen levels become more depleted below 5 mg/l. This warm saline lens may increase with tidal overwash and elevate water temperatures throughout the lagoon to worsen steelhead habitat conditions.

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DISCUSSION OF SOUTH-CENTRAL CALIFORNIA COAST STEELHEAD DPS

The steelhead is currently designated as federally Threatened in all naturally spawned populations (and their progeny) in streams from the Pajaro River (inclusive) located in Santa Cruz County, CA, to (but not including) the Santa Maria River (71 FR 833-862) in San Luis Obispo County.

In North America, steelhead are found in Pacific Ocean drainages from southern California to Alaska. In California, known spawning populations are found in coastal streams from Malibu Creek in Los Angeles County to the Smith River near the Oregon border, and in the Sacramento and San Joaquin River systems. The present distribution and abundance of steelhead in California has been greatly reduced from historical levels. In general, steelhead migrate to sea as two year old fish, spend two years in the ocean, and then return to fresh water to spawn. Peak spawning for steelhead occurs from December through April in small streams and tributaries. Unlike Pacific salmon, steelhead do not necessarily die after spawning, although repeat spawning rates are generally low and vary considerably among populations. Steelhead have traditionally been grouped into seasonal runs according to their peak migration period; in California there are well-defined winter, spring, and fall runs.

Survey Results Figure 3 shows all known occurrences of steelhead within the vicinity.

As described above, steelhead are known from the Carmel River and lagoon. Therefore, steelhead is known to occur within the project area.

Critical Habitat The designation of critical habitat for steelhead became effective on September 2, , 2005 (70 FR 52488). The PCE’s of steelhead critical habitat include freshwater spawning sites, freshwater rearing sites, freshwater migration corridors, estuarine areas, nearshore marine areas, and offshore areas. Carmel River and Lagoon is designated critical habitat for steelhead (Figure 3). The lateral extent of critical habitat for steelhead is the width of the stream channel, defined as the ordinary high-water mark as defined by ACOE in 33 CFR 329.11. In areas for which ordinary high-water has not been defined pursuant to 33 CFR 329.11, the width of the stream channel is defined by its bankfull elevation.

Avoidance and Minimization Efforts Implementation of the following measures is recommended to reduce or avoid impacts of project actions to steelhead: 1. All ground disturbing activities within shall be confined to the “work window” of June 1 to October 31, or other dates as determined by NOAA Fisheries, to minimize potential indirect impacts to local fisheries, such as increased sedimentation and subsequent water quality impacts. Protective fencing shall be placed to keep construction vehicles and personnel from impacting steelhead critical habitat adjacent to the project site. Best Management Practices shall

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mi 0 1.5 3 6

km 01.5 3 6

Project Location^_

Steelhead Critical Habitat Steelhead CNDDB Occurrence

Steelhead Occurrences Figure N Within the Vicinity 3 be employed to reduce the transport of sediment from the site into adjacent sensitive fisheries habitat. Erosion control and slope stabilization measures should be implemented to assure that disturbed slopes do not erode. Additionally, all applicable measures outlined in the attached California Department of Fish and Game Avoidance and Minimization Measures (Appendix B) shall be implemented. 2. Grading, excavating, and other activities that involve substantial soil disturbance shall be planned and carried out in consultation with a qualified hydrologist, engineer, or erosion control specialist, and shall utilize standard erosion control and slope stabilization measures in satisfaction of Monterey County erosion control guidelines to minimize erosion of slopes and sedimentation to native vegetation.

Project Effects

EPB Steelhead is known to occur in the Carmel River and Lagoon.. Additionally, Carmel River and lagoon is designated as steelhead critical habitat. The project is a comprehensive approach to restoring natural breaching function within the lagoon while retaining the existing level of flood protection for public and private infrastructure. While there is the potential for direct and indirect impacts associated with the construction of the EPB and SRPS and the implementation of the ISMP, the overwhelming effect of the project on fisheries resources within the lagoon will be beneficial and would result in: 1. A reduction in frequency of annual mechanical breaching of the sandbar will result in reduced frequency of lagoon evacuation, loss of deeper habitat, loss of invertebrate food productivity, reduced chance of juvenile stranding, less premature entry of juveniles to the ocean at smaller size with reduced survival due to higher predation. 2. Prolonged period of rapid growth for lagoon-dwelling steelhead in the fall associated with later first sandbar breach (FSB) in years when initial storms are small, either due to delayed need for mechanical breach for flood control or allowance of delayed natural breach (allowing additional juvenile steelhead growth in the intact, deeper lagoon prior to sandbar breaching, larger size upon entering the ocean and associated increased survival to adulthood by larger juveniles). According to Balance Hydrologics (2013), in 9 of 20 years (45%), storage routing of river flows through the lagoon predicted natural breaching on average 10 days later than the first significant mechanical breaching, with three of the 20 years (15%) likely to have seen a natural FSB on the order of 21 days later. Balance Hydrologics (2013) stated that it would be unlikely for a sustained sandbar closure at flows of about 100 cfs or greater. 3. Maintained flood protection allowing a more productive estuary/lagoon over a longer time frame throughout the rainy season after the FSB (with reduced need or elimination of repeated mechanical breaches through the wet season in years with isolated storm systems) − resulting in longer period of productive pre-smolt steelhead rearing prior to out migrating, larger smolts and increased survival to adult return. 4. Maintained flood protection allowing higher frequency of natural sandbar breaches that are allowed to migrate north or south across the barrier beach, resulting in a higher invert of the outlet channel and a thicker barrier beach over time. With a more diagonal meander of the outlet

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channel over a thicker beach, a more perched outlet channel will develop with reduced tidal saltwater influx and reduced saltwater lens on the estuary bottom while the sandbar is open and when the sandbar closes for the season. This will reduce saltwater stratification that results in high water temperature and low oxygen concentration at depth and will speed the transition to a cooler freshwater lagoon and better water quality in the summer lagoon. 5. Maintained flood protection allowing potentially higher WSL of the lagoon at final sandbar closure for the dry season, improved lagoon habitat over a longer time frame in the dry season for juvenile steelhead rearing due to greater lagoon volume and depth, reduced competition and reduced predation. Juvenile steelhead growth and survival will be enhanced during the summer lagoon phase. 6. Maintained flood protection allowing more natural breaches that will potentially result in a higher barrier beach crest and thicker barrier beach during the summer, which may reduce the infiltration rate of freshwater through the barrier beach during the summer months and retain larger lagoon volume and depth longer into the dry season when freshwater inflow becomes reduced. This will provide deeper and more productive steelhead habitat to increase steelhead growth rate and reduce predation upon steelhead during the summer. 7. Maintained flood protection allowing more natural breaches that will potentially result in a higher barrier beach crest and thicker barrier beach during the summer, which may reduce tidal overwash in the fall. This will reduce the thickness of the saltwater lens forming afterwards in the lagoon, reduce saltwater stratification and improve water quality with cooler water temperature and higher oxygen concentrations at depth for steelhead after overwash events.

SRPS 1. SRPS will allow more northerly breaches of the barrier beach during the rainy season than existing condition (northerly breach is currently prevented or discouraged to protect road). The result will be improved estuary habitat (deeper) and higher juvenile steelhead growth rate, larger size upon entering the ocean and better survival to adulthood. According to Moffat and Nichol (2013), bedrock sills underlie the beach along both the north and south edges. So, scour by migrating channels or channels intentionally opened along edges would be less than when channels are excavated through the central portion of the beach. With the relatively long channel alignments, further limited by the sills north and south of the river mouth, the drawdown is extended over a longer period, which may reduce juvenile stranding and allow more pre-smolts to remain in the estuary. 2. The SRPS will allow more natural beach barrier dynamics with more northerly breaches, resulting in the residual low point of the barrier beach at the end of the rainy season to be to the north instead of the residual depressed elevation being more to the south from more southerly mechanical breaches- result is greater likelihood of a more diagonal outlet channel to develop to the north, leading to a higher invert to the outlet channel, especially late in the rainy season and after the last stormflow event, and increased area of deeper, higher quality estuary habitat (> 3 feet), larger invertebrate populations, reduced competition for food, higher juvenile growth rate, larger size upon entering the ocean and better survival to adult return. According to Moffat and Nichols (2013), local fisheries groups and agencies have preferred a northern meandering outlet

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channel alignment because, in the past, when the river channel migrated northwards, it reduced the rate and amount of drawdown (drop in lagoon water levels before and after a breach to the ocean) and subsequent loss of threatened juvenile steelhead that get flushed out to sea, as compared to when the channel flows along the southerly and westerly outlet channel (James, 2005). According to Moffat and Nichol (2013), an elongated channel forms to the north along the beach in half of the years of observation (James, 2005) and either natural breaching or channel migration is expected to tend towards the northern alignment since the antecedent, lowered beach alignment has not recovered to typical berm heights and widths (Thornton, 2005). The lower berm elevations to the north, due to milder beach slope and finer sediment, also favor natural breaching or channel migration towards the northern portion of the beach; however, this varies greatly from year to year and depends on wave energy arriving over the winter/spring seasons.

ISMP 1. Actual excavation of the sand to make the outlet channel will begin when the water level in the Lagoon reaches elevation 13.27 feet (NGVD88). This is higher than previous mechanical breaching history, potentially delaying the date of initial sandbar breaching and prolonging the closed lagoon phase and allowing greater steelhead growth prior to entering the ocean and greater survival to adulthood. 2. Mechanical sandbar closure at a higher lagoon WSE if done outside the primary adult spawning migration window (January 1─April 1) and outside the primary smolt out-migration window (April 1─May 31) to reduce evacuation of lagoon/estuary volume and increase habitat depth in the early winter estuary and summer lagoon to promote deeper and higher quality rearing habitat for pre-smolts and over-summering juvenile steelhead that will grow to smolt size and increase juvenile number reaching adulthood with improved water quality.

Project Impacts Direct mortality of this species may occur associated with the mechanical breaching actions described in the ISMP. Additionally, indirect impacts to steelhead critical habitat may result from sedimentation and contamination as a result of erosion during construction activities. The project is likely to adversely affect individual steelhead and is likely to affect but not adversely modify steelhead critical habitat. Specific impacts could include:

Impacts potentially resulting from the EPB: 1. During construction− trapping juvenile steelhead in standing water beyond the footprint of the EBP if the wetted marsh continuous with the lagoon is within the work area. 2. During construction− reduced water quality in the summer lagoon resulting from high turbidity and introduction of hydrogen sulfide from disturbance of decomposing lagoon bottom material.

3. Loss of emergent marsh vegetation during excavation that provides steelhead rearing escape cover and loss of rearing habitat

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Impacts potentially resulting from the SRPS 1. During construction− increased turbidity (reduced water quality) to summer lagoon during sand excavation required to bury riprap. Loss of water clarity will reduced juvenile steelhead feeding efficiency and reduced juvenile steelhead growth rate, ultimate size and survival to adulthood.

Impacts potentially resulting from the ISMP

While the impacts listed below are possible in the short term, the rigorous procedures embedded within the ISMP will avoid and minimize these impacts to the greatest extent feasible while providing a net benefit to special status wildlife species and sensitive habitats in facilitating the implementation of the EPB and SRPS. 1. From mechanical sandbar breaching− loss of juvenile steelhead rearing habitat, potential stranding of juvenile steelhead, increased predation upon juvenile steelhead that remain in the shallower estuary, premature flushing of juvenile steelhead into the ocean to cause osmotic stress and mortality or reduced survival to adulthood due to smaller size, dislocation of some juveniles into sub-optimal stream habitat above the estuary to reduce growth rate and/or survival rate, attraction of adult steelhead into the estuary and stranding them with insufficient streamflow to migrate to spawning reaches. 2. From winter/spring (wet season) mechanical sandbar closure− potential interference with adult steelhead migration (January−March), potential water quality deterioration in the closed lagoon after mechanical closure and loss of steelhead lagoon habitat resulting from saltwater stratification and increased BOD after mechanical sandbar closure. 3. From premature mechanical, final closing of the outlet channel to create a closed lagoon for the dry season before or during the primary smolt out-migration period (April 1─May 31). The impact is the potential for trapping of a significant proportion of the out-migrating smolt population in the summer lagoon and subsequent increased mortality rate in summer lagoon. The anticipated impact will be greater the earlier the mechanical closure occurs. Subsequent increased mortality rate of trapped smolts in the summer lagoon will occur from 1) potentially critically high water temperature conditions, especially in a dry year, 2) high bird and striped bass predation under shallow lagoon conditions, especially in a dry year, 3) slowed steelhead growth rate compared to that expected in ocean conditions, experiencing food competition with YOY steelhead in the lagoon, 4) delayed developmental time from juvenile to adulthood to increase mortality rate. Refer to MPWMD Carmel River smolt down-migrant trapping data for 1999, 2007 and 2013; Smith-Alley San Lorenzo River smolt trapping data from 1987-88 and assume 2-4 weeks of residence time in the estuary of pre-smolts before entering the ocean. According to James (2005), the final seasonal closure (FSC) prior to the imposed mechanical breaching which began in 2006 typically occurred when river inflows receded to between 10 and 20 cfs. Data over the period 1991 through 2005 when the lagoon was believed to have closed naturally, indicated that the sandbar closed at approximately 15 cfs and subsequently filled to a maximum elevation of 9.44 (NAVD88) (G. James pers. comm.). G. James (MPWMD hydrologist; pers. comm.)believed, but could not confirm, that beginning in Water Year (WY) 2006, mechanical closure efforts began with closures around 20 cfs, with the lagoon reaching a maximum elevation of 10.74 (NAVD88). From limited data between WY1993 and WY 2005, the FSC occurred

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approximately 5 days after stream inflow had diminished from 20 cfs to 15 cfs. Therefore, natural FSC would allow out-migrating smolts about 5 extra days to exit the estuary compared to a mechanical FSC at 20 cfs, based on the data analyzed.

Modifications to the Project to Mitigate Potentially Negative Effects The project has been designed to reduce impacts to steelhead and steelhead critical habitat to the greatest extent feasible. The following measures are recommended to mitigate the temporary impacts to steelhead from vegetation removal and ensure no reduction in habitat value will occur subsequent to construction: 1. All disturbed areas shall be revegetated, according to the Revegetation Plan prepared for the project, using local stock of native species appropriate for the habitat disturbed.

The process to complete technical feasibility studies, design, environmental review, permitting, and construction is estimated to take up to five years. In the interim, the County has developed the ISMP for managing the Lagoon including winter openings and summer closure in the best possible manner that reduces potential impacts to both wildlife and property.

The ISMP generally includes the following: 1. Sand bags: As a first course of action ahead of the rainy season, generally defined as beginning October 15, and before mechanically managing the sandbar, the County will stockpile sand and place sand bags along the property boundary of State Parks and homes along the north end of the Carmel Lagoon (Camino Real, River Park Place, Monte Verde Street, and 16th Avenue). This action is subject to receiving permission from all of the property owners. The County will make it clear to homeowners that management of the sandbar is a last resort and that sandbag placement is a crucial component of flood control. 2. Public Outreach: The County will initiate public outreach to warn homeowners so they take appropriate precautions to protect their property during the rainy season (October 15 – April 15). Public outreach will include education on the effect of manual breaches completed by members of the community. This is a carefully managed system and unpermitted manual breaches are extremely harmful and illegal. The County will also make best efforts to keep interested parties informed of actions taken through the rainy season; however, the County’s first priority is communication with the USACE and NMFS. 3. Sandbar management: The County, after receiving appropriate approvals from permitting agencies, will manage the sandbar for flood protection (e.g., mechanical breaching). Any such work would be performed only when necessary – based on pre-determined river and/or tide conditions – to prevent flooding of homes and would be implemented in a manner that would minimize impacts to S-CCC steelhead and their habitat. 4. Re-establishment/Summer Management: The County would assure any outlet channel work performed during the winter is closed off and the sandbar restores at the conclusion of the rainy season, which is generally defined as April 15. In recent years the sandbar has been closed off when stream inflow diminishes to 20 cfs, even if this occurs before April 15. The intent of the summer sandbar channel closure is to promote habitat for listed species throughout the summer months. However, the assumption that early closure will promote better habitat for a longer Fishery Analysis for The Carmel River-Lagoon Biological Assessment Report – January 2014 D.W. ALLEY & Associates Page 42

period in the summer has not been clearly substantiated. And, even if better habitat is provided longer into the dry season, if the minimum lagoon volume is reached well before the rainy season begins and poor water quality ensues, the overall mortality rate for trapped smolts may not be increased for the dry season with an initially slightly larger lagoon volume resulting from mechanical closure. Therefore, with the present uncertainties as to the benefit of mechanically closing the beach berm before it naturally would occur, the best mitigation for the impact of shortening the smolt out-migration period earlier than June 1 is to continue mechanical closure as part of the ISMP, but then rescue as many smolts as possible (those juveniles exhibiting smolt color characteristics) that are trapped in the lagoon after mechanical closure and release them immediately into the ocean. It is the opinion of J.C. Garza (NOAA Fisheries research biologist; pers. comm.) that these smolts will transition successfully to ocean salinity conditions. We recommend that if stream inflow declined to 20 cfs before June 1, then seining be done to rescue smolts in early to mid-May or when stream inflow to the lagoon ceases for the dry season, whichever occurs first.

Supporting Background Information According to G. James (MPWMD hydrologist; recent pers. comm.), it seems logical that beginning the dry season with a lower lagoon level will result in low lagoon levels sooner in the dry season. However, how much sooner is unknown, as well as whether this delay to reaching the minimum habitat depth will increase survival of trapped smolts until the rainy season begins. As stated earlier (James, pers. comm.), comparing the maximum lagoon depth after mechanical sandbar closure to previous natural closures indicated an initial lagoon water surface elevation (WSL) approximately 1.3 feet higher with the mechanical closure, which would result in more water volume stored behind the beach berm initially at the beginning of the lagoon phase. Recent data, according to James (recent pers. comm.) indicated that a net 8-10 cfs or more can seep through the closed beach berm. Therefore, if the inflow is less than 10 cfs at FSC, the lagoon will not fill. However, seepage rate declines as hydraulic head decreases as the lagoon shallows. James (2005) stated that after baseflow receded below 8 cfs, the lagoon dropped 3-4 feet in elevation over a 1-2 month period until reaching a minimum level in August or less often, September. According to James (2005), this minimum level is determined primarily by local water table elevation and subsurface flow into the lagoon that limit further decline, with other factors that include ocean water seepage through the beach bar into the lagoon during high tides and the presence of bedrock at the mouth that serves as a barrier to retain lagoon water. But the rate at which the lagoon level declines is difficult to predict. According to James (recent pers. comm.), it takes about 90 days on average in “critically dry” to “normal” years for the lagoon to reach the dry season low, usually in August, after FSC. So, seepage rate through the beach berm declines through the dry season, and the minimum occurs during one of the warmest summer months, August, well before the next rainy season begins. According to James (recent pers. comm.), the factors that seem to determine when the minimum lagoon WSL is reached likely include but are not limited to: maximum post FSC lagoon level and what time of year this occurs, quantity of surface and subsurface inflow, seepage rate through the beach berm, local evapotranspiration, local fresh water table elevation, humidity, temperature and whether or not a high surf event fills the lagoon (which typically occurs in September which terminates the summertime downward water level trend), and other unknown factors. It is important to restate Fishery Analysis for The Carmel River-Lagoon Biological Assessment Report – January 2014 D.W. ALLEY & Associates Page 43

that tidal overwash will likely result in stratified water quality conditions of oxygen, temperature and salinity that may become stressful for juvenile steelhead and may restrict them to the upper water column where they are more vulnerable to predation.

Furthermore, James (pers. comm.) has not thoroughly analyzed whether starting out with a higher lagoon WSL after FSC will result in a higher minimum lagoon level later in the summer. He believes this to be the case, but stated that streamflow persistence would play a significant role. We suspect that many of the factors that determine when the minimum lagoon level is reached also help to determine the height of the minimum lagoon level. The relative importance of the initial lagoon WSL in determining the minimum lagoon WSL for the dry period has not been verified.

Monitoring and Reporting A monitoring and reporting program will be implemented to document the effects of the ISMP and inform an adaptive management approach during the permit duration. The monitoring program will assess steelhead rearing conditions and relative numbers, distribution and degree of smoltification of steelhead throughout the year and in response to lagoon sandbar management activities. Monitoring will include the following:

1. Flow: River flows will be monitored throughout the permit period, including at the 2-week water quality monitoring intervals during the dry season. River flows will be monitored at the USGS Carmel River Gauge near Carmel. Presence/ absence of lagoon inflow from the River will be documented during the 2-week water quality monitorings through the dry season and at the times of sandbar management activities.

2. Lagoon Opening and Closing: Lagoon opening and closing will be monitored and recorded throughout the permit period. Lagoon surface elevation will be monitored using the MPWMD instrumentation located in the South Arm. Tidal conditions previous to, during and post opening and closing will be recorded from information available from NOAA’s National Ocean Service and National Water Level Information Network.

3. Bathymetry: A bathymetric survey will be conducted annually in the main lagoon embayment, the north arm, the south arm, and in the Odello arm to evaluate the extent and distribution of deeper water habitat that might be utilized by steelhead during the dry season. The total area with depths 1 meter or greater will be estimated and mapped for the lagoon. Annually, the survey will be conducted before sandbar management activities occur to determine the distribution of potential rearing areas in the lagoon and how the sandbar management activities influence depth characteristics and alter potential steelhead rearing habitat. This information will be used to determine possible annual changes in lagoon volume, rearing habitat, and the selection of water quality monitoring stations (see 5. below). The lagoon stage-volume relationship will be updated as needed during the permit period.

4. Sandbar Elevation: Monthly during the wet season and previous to the initial sandbar management activities of the season, a simple topographic survey along the length of the sandbar

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will be conducted to document beach crest elevation and sandbar width. This information will be used to plan management strategies, design lagoon outlet channel configurations, and predict the likelihood of flooding, plus record the response of the sandbar and outlet channel to management activities, tidal influence and river inflows to the lagoon.

5. Water Quality Monitoring: At 2-week intervals from the time of final sandbar closure for the dry season to the first sandbar breach of the rainy season, lagoon water quality parameters including salinity, conductivity, temperature, dissolved oxygen and secchi depth (indicator of turbidity) will be measured at a minimum of five stations within the lagoon: near the mouth, at the upper extent of the lagoon, in the central area of the lagoon, and at least one location in each of the north and south arms at the deepest locations. Water quality measurements will be made at 0.25 m increments through the water column from the water surface to, and including, the bottom at each monitoring interval. The water surface elevation of the lagoon will be measured at existing gages each monitoring interval The monitoring intervals will capture major transitions in river flow, saltwater input, and changes in lagoon stage as a result of initial and subsequent sandbar management activities and natural opening and closure of the sandbar.

Winter (Time of first mechanical sandbar breaching activity of the rainy season through the rainy season to final sandbar closure for the dry season) - Monitoring will be conducted prior to and following, as closely as is safely practical, the initial sandbar management activities of the water year and at the time of each succeeding mechanical breaching through the rainy season. The same 5 monitoring stations and parameters included during the dry season will be used, including the gage height. A measurement of the seawater (ocean) salinity will also be taken after each breaching.

6. Steelhead Monitoring: Fall (October or November) - Sampling will be conducted to evaluate steelhead distribution, abundance, and condition after the summer/fall rearing period and before lagoon sandbar management activities may occur. Mark-recapture population estimates will be completed. Steelhead will be captured with a bag seine approximately 35 meters long (longer ones are more difficult to utilize) in the main lagoon embayment for population estimates. Sampling around the lagoon periphery and arms will be conducted with smaller, 30-foot long beach seines where capture gear is effective in an attempt to document steelhead presence in different areas. If required by NMFS, underwater observation and enumeration may be incorporated where fish capture is infeasible. Captured fish will be measured to length and condition will be described relative to advancement of smoltification (presence/absence of parr marks and body/fin coloration) and the incidence of external parasites or abnormalities. Scales will be collected from a subset of individuals and analyzed to determine age class. Water quality measurements similar to those taken at 2-week intervals will be taken in the main embayment and at peripheral locations when fish sampling occurs. Fish will be released at capture sites. All other fish species captured will be identified and enumerated. Numbers of steelhead will be recorded for each area sampled in order to determine where steelhead may be congregating in the lagoon. A fish sampling protocol will be submitted to NMFS by September 1 of each year prior to annual lagoon flood management activities for approval. Additional sampling of steelhead in the spring will be unwarranted because timing of smolt migration has been well documented from past

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down-migrant smolt trapping, and unnecessary take of steelhead should be avoided. Additional steelhead sampling in summer will be unwarranted because population size and fish lengths near the end of the summer/fall rearing season and prior to sandbar management activities are the critical monitoring parameters that indicate level of survival through the dry season and success of summer/ fall management activities. Unnecessary take from mid-summer sampling should be avoided.

Winter (October through March) - During the initial sandbar management activities of the water year, a NMFS approved biological monitor will conduct observations of areas where fish were detected previous to the sandbar management activities (as documented by fall fish sampling). Observations will be made to detect loss of rearing habitat and fish mortalities that may result as a consequence of isolating shallow pools with possible stranding, changes in water quality and loss of habitat 1 meter or greater in depth.

During and directly following sandbar management, observations of any recently dewatered areas will be conducted to estimate the degree to which fish stranding may occur. The locations of any observed steelhead mortalities and stranded fish will be mapped.

Reporting Recommendations Two annual reports will be prepared each year. One report will cover wet season monitoring from the date of initial sandbar management activities in the fall/winter to the date of final sandbar closure for the dry season in late spring/early summer. The second report will cover dry season monitoring from the date of final sandbar closure for the dry season until the initial sandbar management activities in the fall/winter. These reports are due and deliverable to NMFS within 2 months of the final monitoring date for each monitoring period to provide adequate time for adaptive management strategies to be implemented. The reports will summarize the monitoring activities, the chronology of sandbar opening and closing with streamflow estimates at those times, lagoon elevations throughout the year in response to management activities, and the relationship of river inflows to opening and closing of the lagoon and lagoon water surface elevations through the dry season, and the influence of management activities on surrounding and upstream groundwater levels. The reports will analyze lagoon water quality parameters, and the relative numbers, distribution and abundance of steelhead present in the lagoon in relation to lagoon opening and closure.

Cumulative Effects (ESA) Cumulative effects include the effects of future state, tribal, and local, or private actions that are reasonably certain to occur in the action area considered in this BA. Future federal actions that are unrelated to the proposed action are not considered in this section because they would require separate consultation pursuant to Section 7 of the federal ESA. There are no known non-federal future actions that are reasonably certain to occur in the action area that will have an effect on steelhead.

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CONCLUSIONS AND DETERMINATIONS

Conclusions Steelhead are known to occur in the Carmel River and lagoon. The project has been designed to avoid impacts to steelhead to the greatest extent feasible, although some areas of riparian and wetland habitat will be impacted by project activities. Impacts could include potential take of steelhead as a result of EPB and SRPS construction activities and implementation of the ISMP.

Determination The Ecological Protective Barrier (preferred alternative 2a) may affect, but is not likely to adversely affect steelhead in the action area, with the implementation of the avoidance and minimization measures included in this document that isolate the construction area, with revegetation of wetland vegetation after construction.

The Scenic Drive Protection Structure (preferred alternative 1) may affect, but is not likely to adversely affect steelhead in the action area with the implementation of the avoidance and minimization measures included in this document that isolate the construction area.

The Draft Interim Sandbar Management Plan may adversely affect steelhead in the action area due to mechanical breaching of the barrier beach for flood control purposes. However, potential impacts of mechanical sandbar closure after stormflows in the rainy season can be minimized when breaching occurs prior to January 1 by rapidly closing the sandbar after threat of flooding subsides and before kelp and seagrass can wash into the estuary; avoiding mechanical sandbar closure January 1. Potential impacts of mechanical sandbar closure at the end of the rainy season may be minimized by either constructing an outlet channel to the ocean through the sandbar that insures steelhead smolt passage or by postponing any mechanical closure until after most smolt out-migration is complete, June 1.

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LITERATURE CITED AND PERSONAL COMMUNICATIONS

Alabaster, J.S. 1962. The effect of heated effluents on fish. Int. J. Air Water Poll. 7: 541-563. (Cited by Kubicek and Price 1976).

Alley, D.W. 1990. Instream Flow Analysis of Steelhead Spawning and Rearing Habitat between San Clemente and Los Padres Reservoirs, Monterey County, California. Prepared for the Monterey Peninsula Water Management District.

Alley, D.W. 1991. Instream Flow Analysis of Steelhead Spawning Habitat Below San Clemente Dam, Monterey County, California. Prepared for the Monterey Peninsula Water Management District.

Alley, D.W. 1992. Soquel Creek Lagoon Monitoring Report, 1990-91. Prepared for the City of Capitola by D.W. ALLEY & Associates.

Alley, D.W. 1995a. Instream Flow Analysis of Steelhead Spawning Habitat in the Proposed Inundation Zone of the New Los Padres Dam, Monterey County, California. Prepared for the Monterey Peninsula Water Management District.

Alley, D.W. 1995b. Monitoring Report, 1993-1994, Lagoon Water Quality for Fish, Streamflow Measurements, Fish Sampling and Passage Conditions in San Simeon and Santa Rosa Creeks, San Luis Obispo County, California. Prepared for Cambria Community Services District by D.W. ALLEY & Associates.

Alley, D.W. 1997a. Baseline Fish Sampling, Water Quality Monitoring and Observation of Lagoon Conditions Before Sandbar Breaching at Carmel River Lagoon, Monterey County, California, 1996, Prior to Excavation of the South Arm. Prepared for Smith & Reynolds, Erosion Control, Inc. by D.W. ALLEY & Associates.

Alley, D.W. 1997b. Monitoring Results for San Simeon and Santa Rosa Creeks in 1995 and 1996: Water Quality Conditions in Lagoons, Streamflow Measurements, Fish Sampling in Lagoons, and Steelhead Censusing in the Upper Watersheds, San Luis Obispo County, California. Prepared for Cambria Community Services District by D.W. ALLEY & Associates.

Alley, D.W. 2008. Santa Rosa Creek Fishery Summary, Habitat Conditions, Watershed Management Guidelines and Enhancement Goals, Prepared for the Land Conservancy of San Luis Obispo County by D.W. ALLEY & Associates.

Alley, D.W. 2013a. 2012 Soquel Creek Lagoon Monitoring Report. Prepared for the City of Capitola by D.W. ALLEY & Associates.

Fishery Analysis for The Carmel River-Lagoon Biological Assessment Report – January 2014 D.W. ALLEY & Associates Page 48

Alley, D.W. 2013b. 2012 SUMMARY REPORT− Juvenile Steelhead Densities in the San Lorenzo, Soquel, Aptos and Corralitos Watersheds, Santa Cruz County, CA. Prepared for The County of Santa Cruz Environmental Health Department by D.W. ALLEY & Associates.

Alley, D.W., K Lyons and S. Chartrand. 2004. 2004 Soquel Creek Lagoon Management and Enhancement Plan Update. Prepared for the City of Capitola by D.W. ALLEY & Associates.

Balance Hydrologics, Inc. 2013. Memorandum. The Geomorphic Role of Riverine Processes in Carmel Lagoon Water Surface Elevation and Sand Bar Breaching Dynamics. Prepared under contract with Denise Duffy & Assoc. for Monterey County Water Res. Agency.

Beck, N. E. Fruend and M. Mathias. 2006. Comparative Lagoon Ecological Assessment Project (CLEAP). Prepared for the California Coastal Conservancy by 2ND NATURE, LLC.

Charlon, N., B. Barbier and L. Bonnet. 1970. Resistance de la truite arc-en-ciel (Salmo gairdneri Richardson) a des variations brusques de temperature. Ann. Hydrobiol. 1: 73-89. (Cited by Kubicek and Price 1976).

Dettman, David H. 1984. Appendix A. The Carmel River Lagoon and Its Use by Steelhead. Contained in Assessment of the Carmel River Steelhead Resource; Its Relationship to Streamflow and to Water Supply Alternatives. D.W. KELLEY & Associates.

Draft Memorandum of Understanding Between County of Monterey, U.S. Army Corps of Engineers and National Marine Fisheries Service Regarding Food Prevention and Habitat Protection at the Carmel Lagoon. 2009.

Garza, John Carlos. PhD. 2014. Personal Communication. Fishery Biologist. National Marine Fisheries Service- Southwest Fisheries Science Center. Santa Cruz, CA.

Habitat Restoration Group. 1989. Soquel Creek Lagoon Management and Enhancement Plan. Prepared for the City of Capitola and California Coastal Conservancy.

H.T. Harvey & Associates Ecological Consultants. 2013. Memorandum: Carmel River Lagoon Ecosystem Protective Barrier and Scenic Road Protection Project, Environmental Assessment Focusing on Biological Evaluations and Permitting Issues, HTH Project # 3420- 01, May 23, 2013.

James, Greg. 2014. Personal Communication. Monterey Peninsula Water Management District Hydrologist. Monterey, CA.

James, G. 2005. Technical Memorandum 05-01− Surface Water Dynamics at the Carmel River Lagoon- Water Years 1991 through 2005. Monterey Peninsula Water Manage. District. Fishery Analysis for The Carmel River-Lagoon Biological Assessment Report – January 2014 D.W. ALLEY & Associates Page 49

Kubicek, P.F. and D.G. Price. 1976. An evaluation of water temperature and its effect on juvenile steelhead trout in geothermally active areas of Big Sulphur Creek. Pacific Gas and Electric Company Department of Engineering Research.

Larson, J., F. Watson, J. Casagrande, and B. Pierce. 2006. Carmel River Lagoon Enhancement Project: Water Quality and Aquatic Wildlife Monitoring, 2005-6. The Watershed Institute, California State University Monterey Bay. Rep. WI-2006-06. (Cited in H.T. Harvey 2013.)

Lumas, E.M. 2006. Water quality monitoring for suitable juvenile Steelhead trout (Oncorhynchus mykiss) habitat in the Carmel River Lagoon during minimal fresh water inflow. California State University at Monterey.

McAfee, W.R. 1966. Rainbow trout. In: Inland Fisheries Management. A. Calhoun (ed.). Calif. Dept. Fish and Game. 546 pp. (Cited by Kubicek and Price 1976).

Moffat and Nichol. 2013. Coastal Engineering Analysis Progress Report- Carmel River Lagoon Biological Assessment. Prepared under contract with Denise Duffy & Associates for Monterey County Water Resources Agency.

Monterey Peninsula Water Management District. 2004-2008. Carmel River Basin Surface Water Quality Data Report.

Monterey Peninsula Water Management District. 2009-2013. Carmel Lagoon/Estuary water quality data collected and reported by month (not all months were available).

Monterey Peninsula Water Management District. 2010-2013. Carmel River Fish Counter Results at San Clemente Dam.

Moyle, P.B. 1976. Inland Fishes of California. Univ. of Calif. Press. Berkeley and Los Angeles, California. ISBN: 0-520- 02975-5. Library of Congress no. 75-3776.

National Marine Fisheries Service. 2005. Endangered and threatened species; designation of critical habitat for seven evolutionarily significant units of pacific salmon and steelhead in California; final rule. Federal Register 70:52630.

National Marine Fisheries Service. 2006. Endangered and threatened species; final listing determinations for 10 Distinct Population Segments of west coast steelhead; final rule. Federal Register 71:834-862.

National Marine Fisheries Service. 2007. 2007 Federal Recovery Outline for the Distinct Population Segment of South-central California Coast Steelhead. Prepared by the National Marine Fisheries Service Southwest Regional Office. September 2007.

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National Marine Fisheries Service. 2012a. The Carmel River reroute and San Clemente Dam Removal Project at the San Clemente Dam on the Carmel River. Biological Opinion to the US Army Corps of Engineers, San Francisco District. National Marine Fisheries Service, Southwest Region.

National Marine Fisheries Service. 2012b. South-Central California Steelhead Recovery Plan Public Review Draft. Southwest Regional Office, National Marine Fisheries Service, Long Beach, CA.

Nelson, Jennifer. 1993. Personal Communication. Salmon and Steelhead Biologist. Calif. Dept. Fish and Game, Monterey, CA. Phone # (831) 688-6768.

Robinson, Mark Adam. 1993. The Distribution and Abundance of Benthic and Epibenthic Macroinvertebrates in a Small Seasonal Central California Lagoon. Master’s Thesis. San Jose State University. Biology Department.

Smith, J.J. and D.W. Alley. 1998. Steelhead smolt trapping data collected by Don Alley and Stafford Lehr on the San Lorenzo River just upstream of the estuary in March−June 1987-88.

Swift, C. C., J. L. Nelson, C. Maslow, and T. Stein. 1989. Biology and distribution of the tidewater goby, Eucyclogobius newberryi (Pisces: Gobiidae) of California. Los Angeles County Museum of Natural History, Contributions to Science 404:1-19.

Whitson Engineers. 2013. Carmel River Lagoon Ecosystem Protective Barrier (EPB) and Scenic Road Protection structure (SRPS) Projects Feasibility Report. Prepared for Monterey County Water Resources Agency and Monterey County Department of Public Works.

Whitson Engineers. 2013. Memorandum. Carmel River Lagoon Ecosystem Protective Barrier Lagoon Stage-Volume-Area Analysis.

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LIST OF CONTACTS AND PERSONAL COMMUNICATIONS

Ed Ballman, Hydrologist, Balance Hydrologics, Inc. [email protected]

Beverly Chaney, Fishery Biologist, MPWMD. [email protected]

David Dettman, Fishery Biologist, Private Consultant and formerly with MPWMD. [email protected]

Carlos Garza, Fishery Biologist, National Marine Fisheries Service, Santa Cruz. [email protected]

Larry Hampson, Engineer, MPWMD. [email protected]

Josh Harwayne, Biologist and Project Manager, Denise Duffy & Associates. [email protected]

Jennifer Nelson, Fishery Biologist, California Department of Fish and Wildlife. [email protected]

Brian LeNeve, Fisherman and President, Carmel River Steelhead Association. [email protected]

Jacqueline Pearson-Meyer, Fishery Biologist, National Marine Fisheries Service, Santa Rosa. [email protected]

Nathaniel Milam, Engineer, Whitson Engineers. [email protected]

Ed Morrison, Public Works Field Supervisor, City of Capitola. [email protected]

Anne Senter, Hydrologist, Balance Hydrologics, Inc. [email protected]

Jerry Smith, Fishery Biologist, San Jose State University. [email protected]

Carl Schreck, Fish Physiologist, Oregon State University. [email protected]

Dilip Trivedi, Engineer, Moffat and Nichol. [email protected]

Kevan Urquhart, Fishery Biologist, MPWMD. [email protected]

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APPENDIX A

Interim Sandbar Management Plan (ISMP)

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EXHIBIT 1

EXHIBIT A INTERIM PLAN AND CRITERIA FOR FLOOD CONTROL AND SUMMER MANAGEMENT OF THE CARMEL RIVER LAGOON

This Interim Plan is being prepared in collaboration between Army Corps of Engineers (in consultation with the NMFS), the USFWS, California Coastal Commission, California Department of Fish and Game, California Department of Parks and Recreation, and County of Monterey (herein after collectively referred to as “Parties”) to establish specific criteria to be used for sandbar management of the Carmel River Lagoon. This Interim Plan is proposed to be in effect for a 5-year period or until the Lagoon Project is complete, whichever is less, while Monterey County pursues a long-term solution designed to avoid mechanically managing the Carmel Lagoon. While this Interim Plan is in place, Monterey County will work with the California Department of Parks and Recreation and other resource agencies to develop long range management strategies to provide for flood protection on the Carmel River which take into consideration and preferably benefit, the natural resource of the Carmel River Lagoon.

ISSUES 1. Flood Damage to Roads, Private Property, and Homes: Monterey County has mechanically managed the sandbar between the Pacific Ocean and the Carmel River Lagoon whenever necessary to prevent flooding to the surrounding area. On March 18, 1992, an elevation study was prepared by Monterey County Public Works. Horizontal control is based on the California Coordinate System Zone 4 and vertical control is based on National Geodetic Vertical Datum (NGVD). This survey/study resulted in a contour map in and around the Carmel River Lagoon for the area which could be subject to inundation, should the Lagoon be allowed to breach naturally at an elevation of 15.87 (NGVD88). Potential flooding impacts of natural breaching without protections include: damage to private property, damage to public infrastructure, and reduced response capabilities for emergency service providers to residents in the area.

On December 10, 1982, Monterey County installed a warning marker in the Carmel River Lagoon as a reference point. The top portion of the marker is painted red. The bottom of the red-painted portion is elevation 11.55 NGVD88. Natural breaching was estimated, based on the lowest beach contour of the March 1992 Survey, to be at approximate elevation 15.87 feet (NGVD88). Water levels in the Lagoon at this elevation would result in the flooding of 2,300 lineal feet of residential street, would place 25 single-family residential units within the limits of inundation, the flooding of one sewer pump station and its collection system, and the flooding of various overhead electrical facilities. Other estimates of natural breaching indicated water levels could reach 14.57 feet (NGVD88) which would also flood about 1,000 lineal feet of streets and utilities and would place approximately 13 single family residential units within the limits of inundation. In January 2008, the Lagoon reached its highest recorded elevation of 12.8 (NVGD29), which equates to 15.57 NGVD88.

Carmel Lagoon MOU Page 9 of 18 USACE/NMFS/County EXHIBIT 1

Since development occurred north of the Lagoon, flooding has historically occurred in the identified limits of inundation. During April 1958 and February 1962, flooding covered the blocks southwest of Sixteenth Avenue and Carmelo streets. In November 1982, three homes were flooded; two on River Park Place and one on Carmelo Street. Records indicate that artificial management of the Lagoon has been performed by one of a number of agencies for quite some time. Monterey County Public Works’ involvement began in 1973.

NOTE: Horizontal control is based on the California Coordinate System Zone 4 and vertical control is based on National Geodetic Vertical Datum (NGVD). Past surveys and existing water level markers utilize the 1929 (NGVD29) datum, so much river flow/flood data exists on this datum. However, FEMA FIRMs have now been updated to a 1988 (NGVD88) datum. As such, the elevation data for this application begins to use the NGVD88 datum for current and future surveys of the Carmel River mouth and lagoon. As a result, there will be a differential of about 2.77 feet between NGVD29 and NGVD88. For example, an elevation for historical data showing 10.0 feet using NGVD29 would now be stated as 12.77 feet using NGVD88. Datum references in this document have been adjusted for the NGVD88.

2. Lagoon Habitat: A detailed description of the Carmel River Lagoon habitat is contained in the "Carmel River Lagoon Enhancement Plan," prepared by John Williams, Ph.D. for the Carmel Steelhead Association, Monterey Peninsula Water Management District (“MPWMD), California State Coastal Conservancy, the Monterey County Water Resources Agency, and in cooperation with the California Department of Parks and Recreation. The timing of artificial sandbar management and the Lagoon water level affects the quality of the Carmel River Lagoon habitat. Nesting habitat at the Lagoon for shorebirds may be adversely impacted by high water levels in the Lagoon. Conversely, aquatic habitat and surrounding wetlands are adversely impacted by low water levels caused by poorly designed artificial sandbar management or reduced flow into the Lagoon.

3. Coastal Dune Habitat: Sandbar management activity requires heavy equipment to be driven onto the beach/sandbar through lands owned and administered by the California Department of Parks and Recreation. This agency is contacted prior to any management actions (see the list of individuals/agencies to contact when opening the river mouth). There is no vegetation in the work area; precautions are taken to minimize damage to the habitat.

A long range plan for the Carmel River Lagoon should define and propose solutions to maintain the optimum water level(s) of the Lagoon. The amount of inflow into the Lagoon during dry months may determine the minimum water level that can be maintained in the Lagoon.

DISCUSSION The Carmel River drains approximately 250 square miles of the Santa Lucia and Sierra de Salinas Mountains; most of the runoff comes from the Santa Lucia Mountains on the southwest side of the watershed. The upper 21 miles of the river flows through steep canyons with little

Carmel Lagoon MOU Page 10 of 18 USACE/NMFS/County EXHIBIT 1 alluvium; but the lower 15 miles of the river flows through the Carmel Valley, with alluvial fill. At Highway 1, the alluvium is 0.6 miles wide and over 150 feet deep. Two small dams on the upper river have little affect on winter flows, but water diversions and wells in the river watershed cause the lower river to go dry in the summer. Flow is measured 3.5 miles upstream from the Lagoon at the "Near Carmel" gauge. No significant tributaries enter the river below this gauge which gives a good approximation of flow into the Lagoon. The annual flow has varied from zero to over 350,000 acre feet, with a mean around 73,170 acre feet since the gauge was installed in 1962. There was no flow to the Lagoon in 1976, 1977, 1988, 1989, or 1990. The "one hundred year flood", which has a one percent (1%) chance of occurring in any future year, is about 29,000 cubic feet per second (cfs).

Without upstream diversions for municipal use and irrigation, the average annual discharge would be over 90,000 acre feet, and there would be continuous inflow to the Lagoon in all but the driest years. Aquifer recharge, also, affects flows into the Lagoon. During the dry season, the Monterey Peninsula gets most of its water from the alluvial aquifer of the Carmel River, drawing down the water table in the lower Carmel Valley and drying up the surface channel. When flows increase in the fall or early winter, recharge to the aquifer is initially very rapid, so that runoff from early storms is strongly attenuated or does not reach the Lagoon at all. Once the aquifer has been recharged, flow to the Lagoon accelerates and response times for action to eliminate potential flooding are greatly reduced.

The level and duration of potential flooding will vary from year-to-year, and sandbar management by County forces during the winter rainy season depends on multiple factors including: beach elevations, high tides, river flows. Flow in the river fluctuates reflecting the seasonal rainfall and diversions, and is highly variable from year to year. Flow into the Lagoon normally ceases between June and August and resumes between November and January. Artificial sandbar management by County forces is designed to reduce potential for flooding as well as deposition of heavy silt loads within the Carmel River Lagoon.

Four gauges exist that provide flow estimations in the Carmel River: 1) Los Padres Dam 2) Esquiline Road Bridge in Robles del Rio 3) Carmel River near Carmel Station upstream of Via Mallorca (U.S. Geological Survey) 4) MPWMD installed a telemetered water level gauge at the Highway One Bridge site that is accessible by telephone modem.

MPWMD has developed a discharge rating table for the Highway One site for flows up to 3,150 cubic feet per second (CFS), based on measurements collected during Winter 1992. Response times for action dictate the need to use the Robles del Rio gauge to establish criteria for mobilization and sandbar management. This gauge provides approximately four to six hours of response time.

PRE-MOBILIZATION Sand Bags. Monterey County would continue to stockpile sand and place sand bags around homes along north end of Carmel Lagoon (Camino Real, River Park Place, Monte Verde Street, 16th Avenue). This action is limited to approval by private homeowners closest to the Carmel

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Lagoon to install sand bags on their property. Monterey County would also place pallets of sand bags at the end of the streets and will place bags within the right of way at the end of streets draining to the Lagoon. With sand bags in place, urban water runoff from the Carmel area above must be pumped over the barrier into the Lagoon.

Public Outreach. Annually in September/October, ahead of the rain season, Monterey County would initiate public outreach to warn homeowners so they take appropriate precautions to protect their property during the winter months. Homeowners will also be informed of the adverse affects associated with sandbar management. Also, homeowners will be informed of the state and federal laws governing activities such as breaches/management within the lagoon and penalties associated with activities if conducted without appropriate approvals.

MOBILIZATION AND MANAGEMENT CRITERIA Criteria for this Interim Plan have been developed to manage the sandbar for flood protection (e.g. channeling). Trigger points include water level within the Lagoon, actual and anticipated river flow rates (in consultation with Monterey Peninsula Water Management District), weather forecasts and tidal forecasts. Any such work would be performed only when necessary - based on pre-determined triggers and upon consultation with NMFS - to prevent flooding of homes and would be implemented in a manner that would minimize impact listed species (e.g. steelhead trout). County will use the following criteria to decide when and how to manage the sandbar:

1. Early season planning: County prefers to manage the Lagoon on the southern end of the beach due to accessibility and historical experience with river flows. Parties agree to discuss options as part of early season planning each year that the Interim Plan is in effect. If it is determined that flows will be managed to the north, during this early season planning meeting triggers (e.g. flow velocities, channel proximity to Scenic Road) will be established for redirecting flow. By October 1 of each year the County, NMFS, and the Corps shall have met and agreed upon sandbar management techniques to be implemented during the upcoming winter months. To inform the discussion the County shall provide a brief description of the lagoon’s configuration include a complete sandbar map at least ten days prior to the meeting. In the meeting, Parties will agree on preferred actions for the upcoming season, including but not limited to: A) management location; B) channel configuration; C) target lagoon water elevations; and D) access (e.g. parking lot protection).

2. Mobilization: County may begin to mobilize for a river mouth sandbar management when any one or more of the following occurs: A) The water level in the Lagoon has reached Elevation 12.77feet (NGVD88) B) Evidence is available that water levels in the Lagoon are rising and that the projected rate of Lagoon water level increase indicates the level will reach 12.77 (NGVD88) within hours. The increase in elevation could be caused by flow the river or by waves over- topping the sandbar. A staff gauge will be installed near the existing warning marker that the rate of water level increase can be estimated.

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C) Carmel River flows reach or exceed approximately 200 cfs, as provided by Water Resources Agency or MPWMD to Public Works via the stream gauges at Las Padres Dam and at Esquiline Road Bridge.

Before management of the sandbar occurs, County shall implement all measures of flood protection (e.g. sand bags) to reduce the flood potential to the surrounding homes and infrastructure to the greatest extent feasible.

3. Sandbar Management: Sandbar Management may be triggered by any one or more of the following conditions: A) Lagoon Water Elevation. Actual excavation of the sand will begin when the water level in the Lagoon reaches elevation 13.27 feet (NGVD88). The warning marker will continue to be utilized and checked periodically when there is water in the Lagoon. This monitoring will be completed by County and MPWMD. Generally the marker is recognized by local residents and they can also provide a warning when the water level is approaching the bottom of the painted red area. Annually, prior to the winter rains and intermittently throughout the winter months, County will confirm the base elevation of the warning marker and new staff gauge. B) River Flows. When river flows or rate of increase in water level in the Lagoon, as estimated on the staff gauge, indicates less than six hours until the water level in the Lagoon reaches 12.77 (NGVD88). When inflow exceeds initial opening outflows, the Lagoon continues to rise long after the actual opening. C) High Tides. Due to the exposed nature of the sandbar's location, large waves can sweep completely over the bar, especially at high tide. Wave over-topping can rapidly increase the water level of the Lagoon as well as increase the sandbar elevation. Wave over- topping also can fill in an existing channel.

Subsequent to the opening action and after high inflows from the river have receded, the Lagoon shall either be allowed to naturally close or remain with an open outlet channel flowing over the beach in a meandering channel that is designed to mute tidal influence and rapid draining of the Lagoon. The Lagoon shall be maintained at a minimum 6-foot water surface elevation. If excessive scour is observed in the constructed outlet channel, the Lagoon shall immediately be closed by the placement of sand that is free of contaminants.

County will monitor the river mouth and Lagoon for water levels, both during and after the channel has been opened, as often as necessary as conditions warrant. A qualified (minimum three years experience with anadromous salmonids) biological fish monitor will be present during the initial opening or closure of the channel and while an outlet channel remains open, the biologist shall monitor the channel twice daily (a.m. and p.m.) to document and fish entrainment, strandings or other occurrences that pose risk to steelhead. If stranded steelhead are observed, the County shall contact NMFS and CDFG to coordinate any necessary fish rescues. Regular updates (bi-weekly) via email or phone call shall be provided to address any action that may be necessary if ‘take’ of steelhead occurs. A report produced by the monitor documenting construction activities and any observation of fish mortalities and/or harm or harassment will be submitted to the Corps and NMFS within two weeks post-construction. Said report shall also

Carmel Lagoon MOU Page 13 of 18 USACE/NMFS/County EXHIBIT 1 outline all implemented measures of flood protection to protect surrounding homes and infrastructures and estimate volume of sand moved.

Prior to work occurring during the nesting season of the snowy plover (e.g. summer closure), a qualified biological monitor will identify any areas that pose risk to the snowy plover. A report produced by the monitor documenting any observation of snowy plover will be submitted to the Corps and USFWS pre-construction. In the event that a snowy plover nest is found, the USFWS shall be contacted before work that may impact the species commences.

County requires approximately 24 to 48 hours, depending on weather conditions and the size of the sandbar, to mobilize and clear a channel through the sandbar with 1-2 bulldozers (D6 Caterpillar). County equipment is driven on the beach for sand management only. Loading and fueling takes place from paved areas to clean sand and contain hazardous materials.

County will usually work during daylight hours when large waves can be seen. In addition, work would occur outside of active rain storms to the greatest extent feasible while maintaining primary goals to prevent flooding impact and/or maintain minimum water levels in the Lagoon. Heavy equipment shall not be operated in open waters of the Lagoon. Loading and fueling will take place from paved areas to clean sand and contain hazardous materials.

LAGOON SUMMER MANAGMENT Water levels will be managed in the Carmel River Lagoon at the beginning of the summer dry season by using heavy equipment to modify the beach that separates the lagoon from the ocean. The objective of this management will be to maintain and enhance habitat for fish and wildlife including steelhead trout and California red-legged frogs by maximizing the volume of fresh water in the lagoon. The enhancement will be accomplished by management of the Carmel River Lagoon’s water level to maximize the volume of freshwater in the lagoon at the beginning of the summer dry season. The goal will be to maximize the lagoon water level up to a maximum elevation of 12.77 feet (National Geodetic Vertical Datum 1988, which is equivalent to 10.00 feet on the NGVD of 1929). A larger, deeper lagoon during the summer/fall period increases the quality and quantity of fish and wildlife habitat. A larger and deeper lagoon at the end of the annual river flow period also increases the chances that the lagoon will maintain adequate volume and quality to sustain healthy conditions for fish and wildlife until river flows resume during the following fall/winter period. Project implementation will include placement of sand to close the opening between the lagoon and the ocean.

Dimensions (sandbarrier width at base and top and elevation) of the sandbarrier to be constructed each summer season will be determined in early May of each year in consultation with the agencies. The County shall implement the closure shortly after sandbarrier dimensions are determined.

BEACH/SAND DUNE RESTORATION The sand dune beach area goes through an annual cycle of change that is driven by seasonal wave action. In the winter, steep, high frequency waves tend to move sand from the beach offshore to a bar, or down the coast. In the summer, the waves are smaller and farther apart, and

Carmel Lagoon MOU Page 14 of 18 USACE/NMFS/County EXHIBIT 1 move the sand from the sandbar back to the beach. If sandbar management is completed early during the winter, this cyclic wave action tends to remove the excavation spoils from the beach.

The County will review the beach area prior to May 15 with State Parks personnel. If spoils have not been removed by normal wave action, the spoils area will be re-contoured to a natural state prior to May 15. The County would assure any channel work performed during the winter is closed off and the sandbar restored at the conclusion of the rain season. This area is traditionally part of the beach and water in this area is expected to subside during the summer months.

As opportunities are provided (e.g. water levels in the Lagoon subside), County may harvest sand from non-wet areas along the beach and stockpile the sand for future use under the Interim Plan. County would consult with appropriate agencies to coordinate appropriate timing for harvesting sand from the beach and moving it to approved areas in order to restore beach access. If an adequate quantity of sand is not available from the subject beach, County may obtain approximately 5,000 cubic yards of sand from a local sand plant in Marina.

In order to gain access to the beach, County received permits to use about 1,000 cubic yards of local sand from a sand plant to create a temporary access from Scenic Road near Carmel River State Beach. When or if access can be returned to the Carmel River Beach State Park parking lot, the temporary access from Scenic Road would be re-contoured so that it does not encourage public access. The slope would be restored using sand already in place – no new sand would be imported.

GENERAL CONDITIONS All work involved with sandbar management will be completed in accordance with the Interim Plan and any conditions placed on this Plan.

County will avoid using heavy equipment within all known areas of cultural resources. If County discovers any previously unknown historic or archaeological remains while accomplishing activity described in the Plan, County shall immediately notify Corps of said findings.

During mobilization and when opening the river mouth, County will provide warning signs, fence, flags, barricades, and flagger, in accordance with the attached Pedestrian Control Plan.

County will issue a news release when sandbar management activity has been completed to warn the public of potential hazards. An area outside the limits of work will be designated for the news media and the public to observe the activity.

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The following permits are needed: AGENCY ACTION State Parks and Recreation Memorandum of Understanding or Temporary Right to Enter California Coastal Commission Coastal Development Permit US Army Corps of Engineers Department of the Army Permit US Fish and Wildlife Service Section 7 consultation National Marine Fisheries Service Section 7 consultation (Biological Opinion) California Department of Fish & Lake and Streambed Alteration Agreement (1600 Permit) Game Regional Water Quality Control 401 Certification Board County of Monterey Emergency Proclamation

CARMEL VALLEY RIVER MOUTH MANAGEMENT NOTIFICATION In order to ensure that timely and accurate information is available to all concerned agencies and the public, Monterey County staff will contact the Notification List at the following times. 1. Upon commencement of mobilization. (An estimate of commencement of actual management operations should be included in this notification) 2. Upon commencement of actual river mouth management operations. (An estimate of completion of river management operations should be included in this notification) 3. Upon completion of river mouth management operations.

Management activities will be followed with a report within two weeks of management activity indicating the extent of the activities and any effect to listed species. All agencies on the Notification List will receive a copy of the report. The following contact list is to be used by the County staff when activities are being governed by this Interim Plan. Failure to make contact during off work hours will be followed with a call at 8:00 a.m. the following morning.

AGENCY CONTACT U. S. Army Corps of Engineers Paula Gill (Cameron Johnson) National Marine Fisheries Services Jacqueline Pearson Meyer (Joyce Ambroise) California Department of Fish & Wildlife Rob Tibstra (Linda Connolly) California Coastal Commission Michael Watson (Dan Carl) California Department of Parks & Recreation 24-Hour Dispatch (Steve Bachman) Monterey Peninsula Water Management District Larry Hampson Monterey County Supervisor Kathleen Lee District 5 Monterey County Resource Management Agency Carl Holm (Dawn Mathes)

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Monterey County RMA-Public Works Shawn Atkins (James “Hop” Essik) Monterey County RMA-Planning Laura Lawrence (Joe Sidor) Monterey County RMA-Building Services Michael Rodriguez (Mark Setterland) Monterey County Water Resources Agency Tom Moss (Rob Johnson) Monterey County Office of Emergency Services Sherrie Collins (Sydney Reade) Monterey Communications Center Call Dispatch U.S. Fish and Wildlife Service Chad Mitcham Regional Water Quality Control Board Jennifer Epp

LONG TERM SOLUTION A long term solution to the problems addressed by this Interim Plan have not yet been determined so Monterey County has applied for permits that include investigations, planning, design, and construction of a coordinated solution. Meanwhile, Monterey County has proposed this Interim (5 years) Plan for flood management of the Carmel Lagoon while a long term solution is prepared, design/plans are prepared, environmental documents are completed and processed, and the projecting term project is constructed. The long term solution for the Lower Carmel River and Carmel Lagoon intends to balance protection of the natural environment with the built environment, including: - Enhance ecological conditions along the Carmel River and within the Carmel Lagoon, including habitat for certain threatened or endangered species (California red-legged frog, Central coast steelhead trout, Western snowy plover, Smith’s blue butterfly) - Protection from flooding; existing homes, commercial businesses, school. - Maintain public infrastructure with anticipated sea-level rise; Highway 1, Scenic Road, State Parks facilities (parking lot, restroom). - Retain beach area for public enjoyment - Create trails for public access

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EXHIBIT B TENTATIVE SCHEDULE

LEAD AGENCIES TARGET DATE FOR MILESTONE (Responsible Agencies) COMPLETION Submit Corps application County September 2012 (Concept EPB + Interim Plan) Adopt MOU County, Corps, and NMFS February 2013 Technical Report/Studies County April 2013 (long-term solution) Concept Design County June 2013 Preferred Alternative (long- term solution) Submit Biological Assessment County July 15, 2013 and preferred EPB/Scenic project Initiate Section 7 Consultation Corps July 22, 2013 w/ USFWS and NMFS Issue Public Notice Corps August 1, 2013 Respond to Public Notice County September 15, 2013 Comments Environmental Review County October 2013 Conclude Section 7 USFWS, NMFS October 1, 2013 Consultations Permit Approvals for Corps* October 15, 2013 Planning, Design and Interim (County) Sandbar Management Plan - Note BOs will include both long-term and interim plan Complete Construction of County September 2020** Preferred Alternative (long- (Parks) term solution) * Also requires a 401 certification from the Regional Water Quality Control Board, 1600 Permit from Department of Fish and Game and Coastal Development Permit from the Coastal Commission. ** Depending on funding

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APPENDIX B

California Department of Fish and Game Avoidance and Minimization Measures

Fishery Analysis for The Carmel River-Lagoon Biological Assessment Report – January 2014 D.W. ALLEY & Associates Page 54

STEELHEAD (Oncorhynchus mykiss)

Project work within the wetted stream shall be limited to the period between June 15 and November 1, or the first significant fall rainfall. This is to take advantage of low stream flows and to avoid the spawning and egg/alevin incubation period of steelhead. Whenever possible, the work period at individual sites shall be further limited to entirely avoid periods when salmonids are present (for example, in a seasonal creek, work will be confined to the period when the stream is dry).

No heavy equipment shall operate in the live stream, except as may be necessary to construct coffer dams to divert stream flow and isolate the work site and to excavate the stored sediments from the stream channel immediately upstream of the road crossing.

Work must be performed in isolation from the flowing stream. If there is any flow when the work is done, the operator shall construct coffer dams upstream and downstream of the excavation site and divert all flow from upstream of the upstream dam to downstream of the downstream dam. The coffer dams may be constructed with clean river gravel or sand bags, and may be sealed with sheet plastic. Upon project completion, sand bags and any sheet plastic shall be removed from the stream in such a manner that would allow for the least disturbance to the substrate. Clean river gravel may be left in the stream, but the coffer dams must be breached to return the stream flow to its natural channel.

For minor actions, where the disturbance to construct coffer dams to isolate the work site would be greater than to complete the action (for example, placement of a single boulder cluster), measures will be put in place immediately downstream of the work site to capture suspended sediment. This may include installation of silt catchment fences across the stream, or placement of a filter berm of clean river gravel. Silt fences and other non-native materials will be removed from the stream following completion of the activity. Gravel berms may be left in place after breaching, provided they do not impede the stream flow or fish passage.

The channel shall not be excavated for the purpose of isolating the workspace from flowing water.

The Operator shall obtain a biologist with all necessary State and Federal permits, to rescue any fish within work sites prior to dewatering. Rescued fish shall be moved to the nearest appropriate site on the stream outside of the work area. A record shall be maintained of all fish rescued and moved, and the record shall be provided to DFG at the completion of the work season.

A Service-approved biologist shall permanently remove from within the project work site, any individuals of exotic species, such as bullfrogs, centrarchid fishes, and non- native crayfish, to the maximum extent possible. The Operator shall have the responsibility that such removals are done in compliance with the California Department of Fish and Game Code.

If it is necessary to divert flow around the work site, either by pump or by gravity flow, the suction end of the intake pipe shall be fitted with fish screens meeting DFG and NMFS criteria to prevent entrainment or impingement of small fish. Any turbid water pumped from the work site itself to maintain it in a dewatered state shall be disposed of in an upland location where it will not drain directly into any stream channel.

Any disturbed banks shall be fully restored upon completion of construction. Revegetation shall be done using locally obtained native species. Planting techniques can include seed casting, hydroseeding, or live planting methods using the techniques in Part XI of the California Salmonid Stream Habitat Restoration Manual.

Suitable large woody debris removed from fish passage barriers that is not used for habitat enhancement, shall be left within the riparian zone so as to provide a source for future recruitment of wood into the stream, reduce surface erosion, contribute to amounts of organic debris in the soil, encourage fungi, provide immediate cover for small terrestrial species, and to speed recovery of native vegetation.

The following measures shall be taken to minimize injury and mortality to listed salmonids resulting from fish relocation and dewatering activities: a) Fish relocation and dewatering activities shall only occur between June 15 and November 1 of each year, b) The Operator shall minimize the amount of wetted stream channel that is dewatered at each individual project site to the fullest extent possible, and c) All electrofishing shall be performed by a qualified fisheries biologist and conducted according to the National Marine Fisheries Service Guidelines for Electrofishing Waters Containing Salmonids Listed under the Endangered Species Act, June 2000.

Installation of the contracted bridge(s) will be of adequate size that it will allow anadromous fish passage at all life stages and is designed to comply with current National Marine Fisheries Service (NMFS) Southwest Region fish passage guidelines.

If for some reason these mitigation measures cannot be implemented, or the project actions proposed at a specific work site cannot be modified to prevent or avoid potential impacts to anadromous salmonids or their habitat, then activity at that work site will be discontinued.

HAZARDS AND HAZARDOUS MATERIALS

The Operator shall have dependable radio or phone communication on-site to be able to report any accidents or fire that might occur.

Heavy equipment that will be used in these activities will be in good condition and will be inspected for leakage of coolant and petroleum products and repaired, if necessary, before work is started.

All equipment operators will be trained in the procedures to be taken should an accident occur. Prior to the commencement of work, the Operator shall provide DFG with a plan allowing for prompt and effective response to any accidental spills. All workers shall be informed of the importance of preventing spills and of the appropriate measures to take should a spill occur.

All activities performed in or near a stream will have absorbent materials designed for spill containment and cleanup at the activity site for use in case of an accidental spill.

All fueling and maintenance of vehicles, other equipment, and staging/storage areas shall be located at least 20 meters from any riparian habitat or water body. The Operator shall ensure contamination of habitat does not occur during such operations.

Any equipment or vehicles driven and/or operated within or adjacent to the stream shall be checked and maintained daily, to prevent leaks or materials that if introduced to water could be deleterious to aquatic life.

Staging and storage areas for equipment, materials, fuels, lubricants, and solvents shall be located outside of the stream’s high water channel and associated riparian area. Stationary equipment such as motors, pumps, generators, compressors, and welders, located within the dry portion of the stream channel or adjacent to the stream, will be positioned over drip-pans.

All internal combustion engines shall be fitted with spark arrestors.

The Operator shall have an appropriate fire extinguisher(s) and fire fighting tools (shovel and axe at a minimum) present at all times when there is a risk of fire.

Vehicles shall not be parked in tall grass or any other location where heat from the exhaust system could ignite a fire.

The Operator shall follow any additional rules the landowner has for fire prevention.

HYDROLOGY AND WATER QUALITY

Work shall be conducted during the period of lowest flow.

If it is necessary to divert water around the work site, unimpeded bypass flows shall be maintained at all times to maintain downstream water quality.

When a dam (any artificial obstruction) is being constructed, maintained, or placed in operation, sufficient water shall at all times be allowed to pass downstream to maintain fishlife bellow the dam pursuant to Fish and Game Code Section 5837.

Debris, soil, silt, bark, rubbish, creosote-treated wood, raw cement/concrete or washings thereof, asphalt, paint or other coating material, oil or other petroleum products, or any other substances which could be hazardous to aquatic life, resulting from project related activities, shall be prevented from contaminating the soil and/or entering the waters of the state. Any of these materials, placed within or where they may enter a stream or lake, by Operator or any party working under contract, or with the permission of the Operator, shall be removed immediately.

Effective erosion control measures shall be in-place at all times during construction. Construction within the 5-year flood plain will not begin until all temporary erosion controls (e.g., straw bales or silt fences that are effectively keyed-in) are in-place down slope of project activities within the riparian area. Erosion control measures shall be maintained throughout the construction period. Adequate erosion control supplies (gravel, straw bales, shovels, etc.) shall be kept at all restoration sites to ensure sediment is kept out of water bodies. Erosion control measures shall be utilized throughout all phases of operation where sediment runoff from exposed slopes threatens to enter waters of the State. At no time shall silt laden runoff be allowed to enter the stream or be placed where it may enter the stream.

Silty/turbid water from the excavation and/or project activities shall not be discharged into the stream, lake, or into storm drains. Such water shall be pumped into a holding facility or into a settling pond located in flat stable areas outside of the stream channel, or sprayed over a large area outside the stream channel to allow for natural filtration of sediments. At no time shall turbid water from the settling ponds be allowed to enter back into the stream channel until water is clear of silt.

Sediment shall be removed from sediment controls once it has reached one-third of the exposed height of the control. Whenever straw bales are used, they shall be staked and dug into the ground six (6) inches. Catch basins shall be maintained so that no more than six (6) inches of sediment depth accumulates within traps or sumps.

Sediment-laden water created by construction, washing or other activities or shall be filtered before it leaves the right-of-way or enters the stream network or an aquatic resource area. Silt fences or other detention methods shall be installed as close as possible to culvert outlets to reduce the amount of sediment entering aquatic systems.

Preparation shall be make so that runoff from steep, erodible surfaces will be diverted into stable areas with little erosion potential.

If continued erosion is likely to occur after construction is completed, then appropriate erosion prevention measures shall be implemented and maintained until erosion has subsided.

Upon project completion, all exposed soil present in and around the project site shall be stabilized within seven (7) days.

Work sites will be winterized at the end of each day when significant rains are forecast that may cause unfinished excavations to erode. Winterization procedures shall supervised by a professional trained in erosion control techniques and involve taking necessary measures to minimize erosion on unfinished work surfaces. Winterization includes the following: smoothing unfinished surfaces to allow water to freely drain across them without concentration or ponding; compacting unfinished surfaces where concentrated runoff may flow with an excavator bucket or similar tool, to minimize surface erosion and the formation of rills; and installation of culverts, silt fences, and other erosion control devices where necessary to convey concentrated water across unfinished surfaces, and trap exposed sediment before it leave the work site.

Mulching and seeding using local native species mix is required on all exposed soil which may deliver sediment to a stream.

Poured concrete shall be excluded from the wetted channel for a period of two (2) weeks after it is poured. During that time the poured concrete shall be kept moist, and runoff shall not be allowed to enter a live stream. Commercial sealants (e.g. Deep Seal, Elasto- Deck BT Reservoir Grade) may be applied to the poured concrete surface where difficulty in excluding water flow for a long period may occur. If sealant is used, water shall be excluded from the site until the sealant is dry.

RIPARIAN VEGETATION

No more than 1/3 of any willow plant shall be harvested annually. Care shall be taken during harvest not to trample or over harvest the willow sources.

Planting of seedlings shall begin after December 1, or when sufficient rainfall has occurred to ensure the best chance of survival of the seedlings, but in no case after April 1.

Building materials and/or construction equipment shall not be stockpiled or stored where they could be washed into the water or where they will cover aquatic or riparian vegetation.

The contractor shall not dump any litter or construction debris within the riparian/stream zone. All such debris and waste shall be picked up daily and properly disposed of at an appropriate site. During all activities at project work sites, all trash that may attract predators shall be properly contained, removed from the work site, and disposed of regularly. Following construction, all trash and construction debris shall be removed from work areas.

The Operator shall retain as many trees and brush as feasible, emphasizing shade producing and bank stabilizing trees and brush.

The Operator shall ensure that the spread or introduction of invasive exotic plants shall be avoided to the maximum extent possible. When practicable, invasive exotic plants at the work site shall be removed.

Use project designs and access points that minimize riparian disturbance without affecting less stable areas, which may increase the risk of channel instability.

Minimize compaction by using equipment that either has (relative to other equipment available) less pressure per square inch on the ground or a greater reach, thus resulting in less compaction or less area overall compacted or disturbed.

At the completion of the project, soil compaction that is not an integral element of the design of a crossing should be de-compacted.

Disturbance or removal of vegetation shall not exceed the minimum necessary to complete operations.

Disturbed and compacted areas shall be revegetated with locally obtained native plant species. The species used should be specific to the project vicinity or the region of the state where the project is located, and comprise a diverse community structure (plantings should include both woody and herbaceous species). Plant at a ratio of two plantings to one removed plant.

Unless otherwise specified, the standard for success is 80 percent survival of plantings or 80 percent ground cover for broadcast planting of seed after a period of three (3) years. If at the end of three (3) years there is less than 80% survival, all dead plants shall be replaced.

RARE PLANTS

Prior to the commencement of work, the Operator will employ one or more of the following protective measures: a) Fencing to prevent accidental disturbance of rare plants during construction, b) On-site monitoring by a qualified biologist during construction to assure that rare plants are not disturbed, and c) Redesign of proposed work to avoid disturbance of rare plants.

If it becomes impossible to implement the project at the work site without potentially significant impacts to rare plants, then activity at that work site will be discontinued.