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Salmon and Steelhead Habitat Limiting Factors Water Resource Inventory Areas 3 and 4, the Skagit and Samish Basins

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Salmon and Steelhead Habitat Limiting Factors Water Resource Inventory Areas 3 and 4, the Skagit and Samish Basins SALMON AND STEELHEAD HABITAT LIMITING FACTORS WATER RESOURCE INVENTORY AREAS 3 AND 4, THE SKAGIT AND SAMISH BASINS By Carol J. Smith, Ph.D. Washington State Conservation Commission Lacey, Washington With a Contributing Chapter by Devin Smith (Skagit System Cooperative) and Tyson Waldo (Northwest Indian Fisheries Commission) 1 Acknowledgements This report was developed by the WRIAs 3 and 4 Technical Advisory Group for Habitat Limiting Factors. This project would not have been possible without their vast expertise and willingness to contribute. The following participants in this project are gratefully thanked and include: Eric Beamer, Skagit System Cooperative Karen Chang, U.S. Forest Service Brady Green, U.S. Forest Service Steve Hinton, Skagit System Cooperative Julie Klacan, WDFW Jeff McGowan, Skagit County Roger Nichols, U.S. Forest Service Ben Perkowski, Skagit Watershed Council Tom Slocum, Skagit Conservation District Dr. Carol Smith, WA Conservation Commission Devin Smith, Skagit System Cooperative Tyson Waldo, NWIFC SSHIAP Bob Warinner, WDFW Stan Zyskowski, National Park Service A special thanks to Ron McFarlane (NWIFC), Tyson Waldo (NWIFC, SSHIAP), Josh Greenberg (Skagit County) and Andrea Nouffke (SSC) for mapping, to Rod Sakrison (DOE) for providing reports, and to Devin Smith (SSC) and Tyson Waldo (NWIFC, SSHIAP) for writing the Fish Access Chapter. I also extend appreciation to Devin Smith (SSC) and Kurt Fresh (NMFS) for compiling and developing the habitat rating standards, to Ed Manary for writing the “Habitat Limiting Factors Background”, and to Tim Beechie and Blake Feist (NMFS) for their sediment supply analysis. Also appreciated are the Stock Chapter reviews from Bob Hayman (SSC), Pete Castle (WDFW), and Ann Blakley (WDFW). 2 EXECUTIVE SUMMARY Introduction In the last few decades, many salmonid populations in Washington State have declined, leading to the inclusion of bull trout and Puget Sound chinook salmon on the Endangered Species List. In response, the Washington State Legislature passed several bills to address the problem in a logical, concerted manner. Two key pieces of legislation (Engrossed Substitute House Bill 2496 and Second Engrossed Second Substitute Senate Bill 5596, now 77RCW) initiated the process towards the development of “Habitat Limiting Factors” reports. This report is the habitat limiting factors report for WRIAs 3 and 4, the Skagit and Samish Basins. It provides a consolidation of existing habitat information in a statewide consistent format, and rates various categories of habitat conditions. The habitat categories include fish habitat access, floodplain, sediment, streambed, riparian, water quality, flow, estuarine and nearshore conditions. Each of those conditions are rated as either “poor”, “fair”, “good”, or “data gap”, based upon a set of standards that are described in the Assessment Chapter. This Executive Summary presents only an overview of the worst habitat problems, but all the habitat ratings are provided in Tables 4 and 5 in the Assessment Chapter. More importantly, detailed discussions for each of these habitat conditions can be found within the Habitat Limiting Factors Chapter of this report. Maps of updated salmonid distribution, floodplain, and nearshore conditions are located in a separate electronic file on this disc. The streams addressed in this report include all anadromous salmonid-producing streams and sloughs from Colony Creek in the north to the boundary with WRIA 5 in the south. The non-anadromous reaches of the basins are not included. Nearshore conditions include the shorelines in WRIA 3, the northeastern shoreline of Whidbey Island, and the northern shore of Camano Island, to fully encompass Skagit Bay. Habitat Conditions in the Skagit Basin Introduction Of all the drainages in Puget Sound, the Skagit is the largest and produces the greatest abundance of salmonids and the greatest number of salmonid stocks. It produces the most abundant chum and pink salmon populations in the contiguous United States, and the largest char population in Puget Sound and possibly the State (Beamer et al. 2000; City of Seattle 2001). The Skagit is also the origin of the most abundant wild chinook salmon populations in Puget Sound. The salmonid habitat conditions in WRIAs 3 and 4 are related to land use. For example, the greater the percentage of state or private land contained within a WAU, the higher the road density (see Sediment Chapter). Road density is often a major indicator of sedimentation and fish blockage impacts, and contributes to hydrologic changes. Because of the link between land use and habitat degradations, it is not surprising that 3 many of the major habitat impacts are located in areas where agriculture, urbanization, and private/state forestry predominates. These include the estuaries, the lower Skagit sub-basin, and the Samish Basin. Habitat Conditions in the Nearshore Environment The nearshore environment is the interface between marine and terrestrial habitats, and extends from the outer limit of the photic zone to coastal landforms such as bluffs, sand spits, and coastal wetlands, including the riparian zone on or adjacent to any of these areas. Compared to estuarine and freshwater habitat, less is known about how alterations to the nearshore environments impact salmonids, resulting in less certainty regarding the benefit and certainty of restoration efforts. In this report, nearshore habitat conditions are rated for a variety of parameters, but the most important locations for restoration and potential benefit of restoration efforts are not well known for many of these conditions. However, protection of currently good nearshore habitat should be a priority. Shoreline modifications (dikes, riprap, etc.) are one of the greatest nearshore impacts in WRIA 3, and “poor” rated areas include the shorelines along east Skagit Bay, Swinomish Channel, Padilla Bay, and north Fidalgo Island. These impacts can disrupt sediment and nutrient transport processes, although no information exists to determine which areas are important for these processes in WRIA 3. Coincident with shoreline hardening is lack of riparian vegetation that could provide shade for forage fish spawning areas. Most of the other parameters rated “good” or “fair” for nearshore conditions in WRIA 3 with a few exceptions. Contaminated sediments are a problem in Padilla Bay, Fidalgo Bay, and Guemes Channel, though overall, sediment quality is much better in the WRIA 3 nearshore environment compared to many other areas in Puget Sound (Long et al. 1999). A few areas rated “poor” for overwater structures (boat ramps, piers, slips, etc.), which are a concern for shading eelgrass habitat and altering fish behavior. The two major overwater sites in WRIA 3 are along the Swinomish Channel and north Fidalgo Island. Habitat Conditions in the WRIA 3 Estuaries The estuarine deltas in this report are the bodies of water adjacent to freshwater systems where saltwater mixes with freshwater. The estuary deltas in WRIA 3 include the Samish, east Padilla, Swinomish Channel, North and South Fork Skagit, central Skagit and Douglas Slough deltas. The loss (72%) of intertidal habitat in the Skagit delta (including the nearby sloughs) has been considerable and is of particular importance to chinook salmon (Beamer et al. 2002a). Dikes have isolated much of the historic delta habitat, and fish-blocking tidegates associated with the dikes are numerous. While many of the tidegates do not allow salmon access, they also prevent adequate tidal flushing. Further impacts to the isolated delta habitat, such as ditching, channelization, filling, riparian loss, and loss of habitat complexity have highly degraded the isolated habitat. 4 The loss and degradation of Skagit estuarine habitat is one of the most important habitat issues for salmonids in the Skagit Basin, and because the Skagit produces the most salmonids and salmonid stocks in Puget Sound, restoration of the Skagit delta habitat and preservation/restoration of nearby non-natal pocket estuarine habitat should be a high priority not just for the basin, but for Washington State. Habitat Conditions in the Lower Skagit Sub-Basin The lower Skagit sub-basin (all streams downstream of the Sauk River confluence except for the Baker River) contains the most highly degraded freshwater salmonid habitat in the Skagit Basin with considerable impacts in every habitat category. Floodplain habitat is an essential type of habitat for salmonid production in the Skagit Basin, and is of particular importance to coho salmon. While the lower Skagit River has the most extensive floodplain area in the two WRIAs at an estimated 108 square miles, degradations have been abundant, especially from dikes and riprap. An estimated 62% of the Skagit River channel length from Sedro Woolley to the mouth has been hydromodified, and only 10% of this length has split channels or island habitat (Duke Engineering 1999; Beamer et al. 2000). An extensive loss of wetland habitat is likely when comparing current known wetlands to hydric soils maps. Road density in the lower Skagit floodplain is excessive at 3.3 mi/mi2 indicating a high level of development in a crucial type of salmonid habitat. Water quality within the lower Skagit River has been degraded by various types of development. Elevated levels of nutrients and chronic levels of lead and copper have been documented in the lower mainstem Skagit River. These are presumably from urban and highway runoff, wastewater treatment, failing septic systems,
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