Upper Yuba River Anadromous Salmonid Reintroduction Plan Prepared by: R2 Resource Consultants, Inc. Redmond, Washington and: Stillwater Sciences, Inc. Berkeley, California In collaboration with: National Marine Fisheries Service Santa Rosa, California February 2014 Upper Yuba River Anadromous Salmonid Reintroduction Plan Prepared by: Noble Hendrix(1), Phil J. Hilgert, Timothy J. Sullivan R2 Resource Consultants, Inc. 15250 N.E. 95th Street Redmond, Washington 98052 and AJ Keith, Jody Lando, and Abel Brumo Stillwater Sciences, Inc. 2855 Telegraph Ave, Suite 400 Berkeley, California 94705 In collaboration with: Richard Wantuck NOAA/National Marine Fisheries Service 777 Sonoma Avenue, Suite 325 Santa Rosa, CA 95404 February 2014 (1) Noble Hendrix can be contacted at QEDA Consulting, LLC, 4007 Densmore Ave N, Seattle, WA 98103 Cover photographs from Yuba County Water Agency (http://www.ycwa.com) and U.S. Army Corp of Engineers (USACE 2012). Photographs show, from top to bottom: Daguerre Point Dam, Englebright Dam, New Bullards Bar Dam, Our House Diversion Dam, and Log Cabin Diversion Dam. NMFS Upper Yuba River Anadromous Salmonid Reintroduction Plan CONTENTS PREFACE .................................................................................................................................. XIV EXECUTIVE SUMMARY ....................................................................................................... XVI 1. INTRODUCTION .....................................................................................................................1 1.1 BACKGROUND AND OBJECTIVE ............................................................................................1 1.2 ACTION AREA ......................................................................................................................6 1.3 LAND USE ............................................................................................................................8 1.4 HYDROLOGY ........................................................................................................................9 1.5 REGULATORY AND MANAGEMENT ISSUES .........................................................................12 1.5.1 Federal ESA and California ESA: Listing Status ...................................................12 1.5.2 Hydropower: Federal Power Act and FERC Licensing ........................................16 1.6 STRUCTURAL FEATURES AND FACILITIES ...........................................................................21 1.6.1 Daguerre Point Dam ..............................................................................................22 1.6.2 Englebright Dam and Reservoir ............................................................................24 1.6.3 New Bullards Bar Dam and Reservoir ..................................................................26 1.6.4 Our House Diversion Dam ....................................................................................29 1.6.5 Log Cabin Diversion Dam .....................................................................................30 2. BIOLOGICAL INFORMATION ............................................................................................32 2.1 CV SPRING-RUN CHINOOK SALMON ..................................................................................32 2.2 CV STEELHEAD ..................................................................................................................33 2.3 GREEN STURGEON ..............................................................................................................34 2.4 OTHER SPECIES ..................................................................................................................36 3. DISTRIBUTION OF EXISTING HABITAT .........................................................................38 4. HABITAT CONNECTIVITY .................................................................................................40 4.1 UPSTREAM CONNECTIVITY.................................................................................................42 4.2 DOWNSTREAM CONNECTIVITY ...........................................................................................45 4.2.1 Reservoirs ..............................................................................................................45 4.2.2 Tributary Collector ................................................................................................47 R2 Resource Consultants, Inc. iii February 2014 NMFS Upper Yuba River Anadromous Salmonid Reintroduction Plan 4.2.3 Forebay Passage ....................................................................................................48 4.2.4 Turbines .................................................................................................................50 4.2.5 Spillways ...............................................................................................................51 4.3 TEMPERATURE CONCERNS .................................................................................................52 4.4 PHASED PASSAGE FACILITIES .............................................................................................53 5. STOCK SELECTION AND GENETIC MANAGEMENT ....................................................61 5.1 INTRODUCTION ...................................................................................................................61 5.2 UPPER YUBA RIVER WATERSHED CHARACTERISTICS ........................................................61 5.2.1 Flow .......................................................................................................................61 5.2.2 Barriers to Anadromy ............................................................................................62 5.2.3 Water Temperature ................................................................................................63 5.3 CENTRAL VALLEY SPRING-RUN CHINOOK SALMON AND STEELHEAD LIFE HISTORIES ......63 5.3.1 Central Valley Spring-run Chinook Salmon ESU .................................................63 5.3.2 California Central Valley Steelhead DPS ..............................................................70 5.4 REINTRODUCTION STRATEGY .............................................................................................71 5.4.1 Recovery Priorities for Central Valley Spring-run Chinook Salmon and Steelhead ...............................................................................................................71 5.4.2 Viable Salmonid Populations ................................................................................72 5.5 POTENTIAL SOURCES OF DONOR STOCK FOR REINTRODUCTION TO THE UPPER YUBA WATERSHED ......................................................................................................................73 5.5.1 Spring-run Chinook Salmon ..................................................................................76 5.5.2 Steelhead ................................................................................................................77 5.5.3 Hatchery Stocks .....................................................................................................77 5.6 STOCK SELECTION CONSIDERATIONS .................................................................................78 5.6.1 Criteria Used by Other Reintroduction Efforts .....................................................78 5.6.2 Genetics .................................................................................................................79 5.6.3 Recommendations and Additional Considerations ...............................................81 6. PRODUCTION POTENTIAL OF YUBA RIVER .................................................................83 6.1 MODELING APPROACH AND MANAGEMENT SCENARIOS ....................................................83 6.1.1 Dry Conditions Scenario .......................................................................................85 R2 Resource Consultants, Inc. iv February 2014 NMFS Upper Yuba River Anadromous Salmonid Reintroduction Plan 6.1.2 Alternative Management Scenarios .......................................................................85 6.2 POPULATION DYNAMICS (POP)..........................................................................................86 6.2.1 POP Module Structure ...........................................................................................86 6.2.2 POP Module Parameterization ..............................................................................92 6.3 SPRING-RUN CHINOOK SALMON RESULTS..........................................................................92 6.3.1 Predicted Distribution of Suitable Habitat ............................................................92 6.3.2 Carrying Capacity Estimates ..................................................................................94 6.3.3 Smolt Production Estimates ..................................................................................96 6.3.4 Summary ................................................................................................................98 6.4 STEELHEAD RESULTS .........................................................................................................98 6.4.1 Predicted Distribution of Suitable Habitat ............................................................98 6.4.2 Carrying Capacity Estimates ................................................................................100