U.S. Fish and Wildlife Service Biological Sampling in the Skokomish River Basin, Washington: Army Corps of Engineers General Investigation July 2011 By Roger Peters, Zhuozhuo Li, Sco Sanders, Roger Tabor, Carrie Cook‐Tabor, and Paul Bakke U.S. Fish & Wildlife Service Washington Fish & Wildlife Office Lacey, Washington Keith Denton and Marn Liermann Naonal Oceanic & Atmospheric Associaon Northwest Fisheries Science Center NOAA Fisheries Seale, Washington Sponsored by U.S. Army Corps of Engineers, in cooperaon with the Skokomish Tribe, Mason County and U.S. Geological Survey Biological Sampling in the Skokomish River Basin, Washington: Army Corps of Engineers General Investigation By R. Peters, M. Li, K. Denton2, M. Liermann2, S. Sanders, R. Tabor, and C. Cook-Tabor P. Bakke Fisheries Division Washington Fish and Wildlife Office U.S. Fish and Wildlife Service Lacey, Washington Northwest Fisheries Science Center2 NOAA Fisheries Seattle, Washington July 7, 2011 ii Acknowledgements Significant contributions to study design, field data collection, data analysis, and writing for this report were made by Jeff Duda (USGS) (Periphyton and Macroinvertebrates), Barry Berejikian and Megan Moore (NOAA) (steelhead acoustic results), which greatly increased the scope and quality of this report. Sarah Morley (NOAA) assisted with the development of the periphyton and macroinvertebrate sampling design and training of field crews, and provided general consultation regarding the implementation of this sampling effort. Field data collection would not have been possible without the assistance of Nathan Hyde, Jamie Sproul, Andy Miller, Sarah Moffitt, Sedge Neil, Eric Myers, Russell Marlow, Ed Hughes, Cara Schildtknecht, Andrew Gima, Dan Spencer, Jeremy Anhalt, Dan Lantz, Jon Lobello, Lindsey Wright, Tracy Leavy, Howard Gearns, Keith Sweeney, Miranda Plumb, Matt Wynn, Anna Baldy, and John Krasowski (all U.S. Fish and Wildlife Service), and Keith Denton (NOAA), and Jeff Duda (USGS). Comments from Pat Cagney, Fred Goetz, Karl Eriksen, Brendan Yuill, C. Klocow (all with USACE), Rich Gieger (Mason County), Brad Thompson (USFWS), George Pess (NOAA), on earlier drafts greatly improved this report. This project was funded by the Army Corps of Engineers. Additional funding was provided by the U.S. Fish and Wildlife Service‟s Washington Fish and Wildlife Office through the Fish and Wildlife Management Assistance Program. iii Table of Contents Acknowledgements ....................................................................................................................... ii Table of Contents ......................................................................................................................... iii List of Figures ............................................................................................................................... vi List of Tables ............................................................................................................................... xv Acronyms .................................................................................................................................. xviii Summary ..................................................................................................................................... xxi Background .......................................................................................................................... xxi Skokomish Basin Condition: Physical Characteristics ....................................................... xxii Skokomish Basin Conditions: Biological Characteristics .................................................. xxv Introduction ................................................................................................................................... 1 Skokomish Basin Condition: Physical Characteristics ............................................................. 5 Drainage Area ......................................................................................................................... 5 Geology ................................................................................................................................... 9 Climate .................................................................................................................................. 10 Hydrology ............................................................................................................................. 10 Disturbance Regime .............................................................................................................. 11 Interaction of Physical Characteristics and Processes .......................................................... 12 Current Habitat Conditions for All Species: Stream Habitat ................................................ 28 Sample Sites ................................................................................................................. 29 Salmonid Habitat Degradation ..................................................................................... 34 Reduced Habitat Availability ............................................................................ 34 Reduced Habitat Connectivity .......................................................................... 39 Reduced Channel Stability ................................................................................ 42 Reduced Habitat Quality ................................................................................... 42 Reduced Riparian Vegetation ........................................................................... 43 Decreased Instream Flows ................................................................................ 47 Increased Summer Temperatures ...................................................................... 48 Reduced LWD .................................................................................................. 52 Reduced Pool Habitat ....................................................................................... 58 Current Habitat Conditions for All Species: Off-Channel Pond Habitat .............................. 69 Current Habitat Conditions for All Species: Estuarine and Nearshore Habitat .................... 84 Skokomish Basin Conditions: Biological Characteristics ....................................................... 87 Primary and Secondary Producers ........................................................................................ 87 Primary Producers: Periphyton .................................................................................... 87 Secondary Producers: Macroinvertebrates ................................................................... 91 iv Linking Primary and Secondary Species Assemblages to Environmental Data .......... 95 Habitat Conditions at Primary and Secondary Sampling Locations .......................... 100 Conclusion: Primary and Secondary Producers ......................................................... 104 Fish Assemblage ................................................................................................................. 104 Juvenile Salmon Habitat Requirements and Status............................................................. 105 General Requirements for all Juvenile Salmonid Species ......................................... 105 Incubation ....................................................................................................... 105 Rearing ............................................................................................................ 107 Physical Characteristics .................................................................................. 107 Productivity and Competition ......................................................................... 107 Predation ......................................................................................................... 108 Seaward migration .......................................................................................... 108 Chinook Salmon .................................................................................................................. 109 Adult ........................................................................................................................... 109 Puget Sound Chinook: Spring ......................................................................... 110 Puget Sound Chinook: Lake Cushman ........................................................... 110 Juvenile ...................................................................................................................... 111 Limiting Factors: Chinook Salmon ............................................................................ 124 Chum Salmon ...................................................................................................................... 126 Adult ........................................................................................................................... 126 Chum – Upper Skokomish Late Fall .............................................................. 126 Chum - Lower Skokomish Fall Chum ............................................................ 126 Chum - Summer Chum ................................................................................... 127 Juvenile ...................................................................................................................... 127 Limiting Factors: Chum Salmon ...............................................................................