Modeling Habitat Capacity and Population Productivity for Spring-run Chinook Salmon and Steelhead in the Upper Yuba River Watershed Technical Report Prepared for National Marine Fisheries Service 777 Sonoma Avenue, Suite 325 Santa Rosa, California 95404 Prepared by Stillwater Sciences 2855 Telegraph Ave., Suite 400 Berkeley, California 94705 February 2012 Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed Suggested citation: Stillwater Sciences. 2012. Modeling habitat capacity and population productivity for spring-run Chinook salmon and steelhead in the Upper Yuba River watershed. Technical Report. Prepared by Stillwater Sciences, Berkeley, California for National Marine Fisheries Service, Santa Rosa, California. February 2012 Stillwater Sciences i Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed Table of Contents EXECUTIVE SUMMARY.....................................................................................................ES-1 1 INTRODUCTION ..................................................................................................................1 1.1 Goals and Objectives ................................................................................................... 1 1.2 Approach...................................................................................................................... 1 1.3 Basin Overview............................................................................................................ 2 2 FOCAL SPECIES...................................................................................................................5 2.1 Spring-run Chinook Salmon ........................................................................................ 5 2.1.1 Status and life history............................................................................................ 5 2.1.2 Conceptual model of key limiting factors ............................................................. 7 2.2 Steelhead...................................................................................................................... 8 2.2.1 Status and life history............................................................................................ 8 2.2.2 Conceptual model of key limiting factors ........................................................... 10 3 RIPPLE MODEL OVERVIEW ..........................................................................................11 4 MODELED SUB-BASINS AND ALTERNATIVE MANAGEMENT SCENARIOS ....12 4.1 Sub-basins.................................................................................................................. 12 4.2 Modeling Scenarios ................................................................................................... 14 4.2.1 Current conditions............................................................................................... 16 4.2.1.1 Spring-run Chinook salmon..................................................................... 16 4.2.1.2 Steelhead.................................................................................................. 18 4.2.2 Alternative Management Scenario 1 ................................................................... 20 4.2.2.1 Spring-run Chinook salmon..................................................................... 20 4.2.2.2 Steelhead.................................................................................................. 21 4.2.3 Alternative Management Scenario 2 ................................................................... 23 4.2.3.1 Spring-run Chinook salmon..................................................................... 23 4.2.3.2 Steelhead.................................................................................................. 24 4.3 Expanded Steelhead Distribution............................................................................... 24 4.3.1 Current conditions............................................................................................... 25 4.3.2 Alternative Management Scenarios 1 and 2........................................................ 26 5 STREAM CHANNEL NETWORK AND HYDRAULIC GEOMETRY ........................27 5.1 Stream Channel Network Development and Attribution........................................... 27 5.2 Hydraulic Geometry .................................................................................................. 28 5.2.1 Current conditions in the upper Yuba River watershed ...................................... 28 5.2.1.1 North Yuba sub-basin .............................................................................. 30 5.2.1.2 Middle Yuba and South Yuba sub-basins................................................ 32 5.2.1.3 Below New Bullards Bar Dam ................................................................ 34 5.2.2 Alternative management scenarios...................................................................... 34 5.3 Application of GEO Module Results......................................................................... 36 February 2012 Stillwater Sciences ii Technical Report Modeling Spring-Run Chinook Salmon and Steelhead in the Upper Yuba River Watershed 6 SPRING-RUN CHINOOK SALMON ................................................................................37 6.1 Habitat Capacity (HAB) ............................................................................................ 37 6.1.1 Methods............................................................................................................... 37 6.1.1.1 Channel gradient and habitat type composition....................................... 37 6.1.1.2 Holding density and usable fraction......................................................... 38 6.1.1.3 Spawning density and usable fraction...................................................... 39 6.1.1.4 Juvenile rearing density and usable fraction............................................ 40 6.1.1.5 Physical habitat thresholds....................................................................... 42 6.1.1.6 Parameterization of Alternative Management Scenarios......................... 42 6.1.2 Results and discussion......................................................................................... 42 6.1.2.1 Predicted distribution of suitable habitat ................................................. 42 6.1.2.2 Carrying capacity estimates ..................................................................... 43 6.2 Population Dynamics (POP)...................................................................................... 46 6.2.1 POP module structure.......................................................................................... 46 6.2.2 POP module parameterization............................................................................. 49 6.2.3 Results and discussion......................................................................................... 49 6.3 Chinook Salmon Model Sensitivity and Uncertainty ................................................ 52 7 STEELHEAD........................................................................................................................53 7.1 Model Assumptions and Structure............................................................................. 53 7.2 Habitat Capacity (HAB) ............................................................................................ 54 7.2.1 Methods............................................................................................................... 54 7.2.1.1 Channel gradient and habitat type composition....................................... 54 7.2.1.2 Spawning density and usable fraction...................................................... 55 7.2.1.3 Summer juvenile rearing density and usable fraction.............................. 56 7.2.1.4 Winter juvenile rearing density and usable fraction ................................ 58 7.2.1.5 Physical habitat thresholds....................................................................... 59 7.2.1.6 Parameterization of Alternative Management Scenarios......................... 60 7.2.2 Results and discussion......................................................................................... 60 7.2.2.1 Predicted distribution of suitable habitat ................................................. 60 7.2.2.2 Carrying capacity estimates ..................................................................... 62 7.3 Smolt Production Estimates....................................................................................... 65 7.3.1 Methods............................................................................................................... 65 7.3.2 Results and discussion......................................................................................... 65 7.4 Steelhead—Model Sensitivity and Uncertainty......................................................... 67 8 MODEL CONSIDERATIONS ............................................................................................67 8.1 Modeling Challenges ................................................................................................. 68 8.2 Model Validation ....................................................................................................... 68 8.3 Recommendations for Model Refinement ................................................................. 69 9 REFERENCES......................................................................................................................70