Synthesis of Salmon Research and Monitoring 1 Acknowledgements Contributors The following persons contributed to the production of this report: Mike Cooksey Peter N. Johnson Paul DeVries Michele Koehler Charles J. Ebel Lynne Melder Frederick A. Goetz Jim Muck Julie Hall Eva Weaver Funding Sources of Lake Washington General Investigation study funding and personnel: • U.S. Army Corps of Engineers Seattle District • Seattle Public Utilities • King Conservation District • King County/Metro • National Marine Fisheries Service • Washington Department of Fish and Wildlife Participants The following persons and organizations participated substantively in the research projects that contributed to this report: • U.S. Army Corps of Engineers: Linda Smith, Chuck Ebel, Fred Goetz, Lynne Melder, Rebecca Jahns, Marian Valentine, Amy Reese, Jeff Dillon, David VanRijn, Bill Nagy, Larry Lawrence, Jim Sadler, John Post, Bill Livermore, and most of the other Hiram M. Chittenden Locks staff • Seattle Public Utilities: Melinda Jones, Jean White, Keith Kurko, Julie Hall, Gail Arnold, Bruce Bachen, Alan Chinn, Rand Little • U.S. Fish and Wildlife Service: Roger Tabor, Mark Celedonia, Howard Gearns, Charles McCoy, Sergio Camacho, and other USFWS staff • King County: Doug Houck, Hans Berge, Francis Sweeney, Gary Yoshida, • Washington Department of Fish and Wildlife: Dave Seiler (retired), Lindsey Fleischer, Chris Waldbillig, Mark Carr, Mike Mizell, Hwa Kim, Clayton Kinsel, Pete Topping, Kelly Kiyohara, Issaquah Creek Hatchery Staff • National Marine Fisheries Service: Steve Achord, Kurt Fresh, Thomas Sibley, Steve Smith, John Williams • Muckleshoot Indian Tribe: Holly Coccoli, Eric Warner, Brian Footen • University of Washington: Dave Beauchamp, Si Simenstad, Jason Toft, Mark Tetrick, Bill Couch • R2 Resource Consultants: Paul DeVries, Karee Oliver, Adam Weybright, Noble Hendrix • Mevatec/BAE Systems: Peter Johnson, Kyle Bouchard, Adrienne Fox, Linda O’Leary, Patricia Pearson, Michael Hanks, Jennie Husby, Mark Vanderven, Gina White • Parametrix: Bob Pfeifer, Pete Lawson, Bill LaVoie • Waterways Experiment Station: Gene Ploskey, John Nestler • Pacific Northwest National Laboratory: Kenneth Ham • Biomark: Dean Park, Scott McCutcheon, Brett Turley, Anthony Carson • Precision Acoustic Systems: lan Wirtz Synthesis of Salmon Research and Monitoring i ii City of Seattle Contents EXECUTIVE SUMMARY 1 1. INTRODUCTION 11 1.1 Organization of this Report 11 1.2 Purpose of Lake Washington General Investigation Study 11 1.2.1 General Investigations with the U.S. Army Corps of Engineers 12 1.2.2 Status of the LWGI 12 2. LAKE WASHINGTON WATERSHED AND FOCUS AREA 15 2.1 General Watershed Description 15 2.2 Historical Context 17 2.3 Lake Washington Modifications 18 2.4 The Ship Canal and Lake Union Modifications 19 2.5 The Locks and Vicinity 20 2.5.1 Physical Features of the Locks 22 2.5.2 Passage Routes 28 2.5.3 Water Management 30 2.5.4 Water Quality Conditions around the Locks 31 2.5.5 Adaptive Management at the Locks 33 2.6 Lake Washington Basin Salmon 34 2.6.1 Stocks 34 2.6.2 Life-History Characteristics 35 3. SUMMARY OF RESEARCH FINDINGS 37 3.1 Juveniles 37 3.1.1 Lake Washington Residency 37 3.1.2 Lake Washington Outmigration 44 3.1.3 Ship Canal and Lake Union Outmigration 45 3.1.4 Passage at the Hiram M. Chittenden Locks (Locks) 54 3.1.5 Estuarine Transition in Salmon and Shilshole Bays 67 3.1.6 Puget Sound Residency 70 3.2 Adults 70 3.2.1 Puget Sound Residency 70 3.2.2 Estuarine Transition 71 3.2.3 Passage at the Locks 71 3.2.4 Ship Canal and Lake Union Migration 85 Synthesis of Salmon Research and Monitoring iii 3.2.5 Lake Washington 90 4. SALMON USE OF THE LAKE WASHINGTON WATERSHED 93 4.1 Conceptual Models for Lake Washington Salmon 93 4.1.1 Chinook Salmon 93 4.1.2 Coho Salmon 96 4.1.3 Sockeye Salmon 100 4.1.4 Steelhead/Rainbow Trout 102 4.2 Climate Change: Adapting Conceptual Models 104 4.2.1 Climate Change and Salmon in the Lake Washington Basin 104 4.2.2 Juvenile Salmon and Regional Climate Change 109 4.2.3 Adult Salmon and Regional Climate Change 109 5. MANAGEMENT ACTIONS AND FURTHER STUDY 111 5.1 Objectives and Actions for Juvenile Salmon 111 5.1.1 Objective: Improve Habitat for Juvenile Salmon in Lake Washington 111 5.1.2 Objective: Improve Habitat for Juvenile Salmon in the Ship Canal and Lake Union 112 5.1.3 Objective: Improve Passage through the Locks for Juvenile Salmon 113 5.1.4 Objective: Decrease Water Temperature and Salinity Gradients between Salmon Bay and the Ship Canal 115 5.2 Objectives and Actions for Adult Salmon 116 5.2.1 Objective: Increase Volitional Pathways between Shilshole Bay and the Ship Canal 116 5.2.2 Objective: Decrease Water Temperature and Salinity Gradients between Shilshole Bay and the Ship Canal 117 5.2.3 Objective: Increase Area of Estuarine Conditions around Locks to Improve Adult Fish Habitat 117 5.2.4 Conflicting Actions 118 6. REFERENCES 119 iv City of Seattle List of Figures Figure 1 Lake Washington Basin Ecosystem Restoration General Investigation (LWGI) study area............................................................................................. 13 Figure 2 The western portion of the Lake Washington watershed and focus area of this report. The Ship Canal system is outlined................................................ 15 Figure 3 The Ship Canal system, as defined for this report. Ship Canal refers collectively to the Montlake Cut, Portage Bay, Lake Union, the Fremont Cut, and Salmon Bay....................................................................................................... 16 Figure 4 Lake Union and Salmon Bay circa 1890. A ridge separated Lake Union and Union Bay and a small stream drained Lake Union into tidally-influenced Salmon Bay ............................................................................................................ 17 Figure 5 Lake Washington and Duwamish drainage basins before 1900 and after 191618 Figure 6 Major physical features of the Locks ......................................................... 23 Figure 7 Major physical features of the Locks. Large lock chamber upper and lower gates are open and middle gate is closed. Small lock chamber is closed. Smolt flumes are operating......................................................................................... 23 Figure 8 Large lock chamber looking downstream toward the middle miter gate during annual dewatering. The filling culvert entrance is shown in the middle with strobe light. The saltwater barrier is shown far right in down position......... 24 Figure 9 Saltwater drain, showing outlet to Puget Sound and pipe to fish ladder........ 26 Figure 10 Fixed weirs (steps) within the fish ladder at the Locks .............................. 28 Figure 11 Migration routes of juvenile salmon through the Locks to the Puget Sound. Solid lines represent passage routes most likely used. Dashed lines represent routes of lesser importance..................................................................... 29 Figure 12 Migration routes of adult salmon through the Locks to Puget Sound. Solid lines are the most likely routes. Dashed lines are less important ........................ 30 Figure 13 Cool water refuge area formed near intake to the saltwater drain at the Locks ............................................................................................................ 32 Figure 14 Average travel speed of juvenile PIT-tagged Chinook salmon between Bear Creek and the Locks. Data are plotted by release date .............................. 46 Figure 15 Nearsurface water temperatures (Celsius) in the Lake Washington Ship Canal during smolt outmigration (2001-2005) at Ballard Bridge and Gasworks sites48 Figure 16 Surface, mid-depth and bottom water temperature (°C) in Ship Canal (spring and summer 2004)................................................................................. 48 Figure 17 Smolt flume detection rates for naturally-produced, juvenile Chinook salmon by date. Top shows fish released in Bear Creek. Bottom shows fish released in the Cedar River. Numbers were adjusted for detection efficiencies................... 50 Figure 18 Smolt flume detection rates for naturally-produced, juvenile coho salmon by date. Top shows fish released in Bear Creek. Bottom shows fish released in Cedar River ........................................................................................... 51 Figure 19 Optional passages for juvenile salmon through the Locks. Fish can only access each pathway at certain depths. Depths are relative to full pool. For the large lock, the saltwater barrier depth is indicated with a lighter blue bar............ 55 Figure 20 Chinook salmon positions at the Locks. Blue indicates no usage and red indicates highest usage. Colors between show a gradient.......................... 57 Figure 21 Coho salmon positions at the Locks. Blue indicates no usage and red indicates the highest usage. Colors between show a gradient.................................. 57 Synthesis of Salmon Research and Monitoring v Figure 22 Diel depth distribution of tagged Chinook salmon smolts at the entrance to the large lock, June-July, 2007. Median proportion of time spent at depth is shown and 10th and 90th percentiles are indicated with error bars....................... 59 Figure 23 Average catch size (blue line is catch per unit effort or CPUE) of natural origin Chinook and coho salmon smolts below the Locks and PIT-tag detection rates in smolt flumes (symbols) in 2001. Estimated release date for each group