April 2019 Conservation Planning Foundation for Restoring Chinook Salmon (Oncorhynchus Tshawytscha) and O. mykiss in the Stanislaus River Contributors and Participants American Rivers: John Cain Anchor QEA, LLC: John Ferguson, Elizabeth Greene, and Michelle L. Ratliff The Bay Institute: Jon Rosenfield and Alison Weber-Stover California Department of Fish and Wildlife: Stephen Louie, John Shelton, and Tim Heyne National Oceanic and Atmospheric Administration: Brian Ellrott, Sierra Franks, Monica Gutierrez, Rhonda Reed, David Swank, Steve Edmundson, and Katherine Schmidt National Oceanic and Atmospheric Administration, University of California, Davis: Rachel Johnson The Nature Conservancy: Jeanette Howard and Julie Zimmerman State Water Resources Control Board: Chris Carr and Daniel Worth Trout Unlimited: Rene Henery University of California, Davis, San Francisco Public Utilities Commission: Ron Yoshiyama U.S. Bureau of Reclamation: Joshua Israel U.S. Fish and Wildlife Service: Paul Cadrett, Ramon Martin, and J.D. Wikert CONSERVATION PLANNING FOUNDATION FOR RESTORING CHINOOK SALMON (ONCORHYNCHUS TSHAWYTSCHA) AND O. MYKISS IN THE STANISLAUS RIVER Contributors and Participants American Rivers: John Cain Anchor QEA, LLC: John Ferguson, Elizabeth Greene, and Michelle L. Ratliff The Bay Institute: Jon Rosenfield and Alison Weber-Stover California Department of Fish and Wildlife: Stephen Louie, John Shelton, and Tim Heyne National Oceanic and Atmospheric Administration: Brian Ellrott, Sierra Franks, Monica Gutierrez, Rhonda Reed, David Swank, Steve Edmundson, and Katie Schmidt National Oceanic and Atmospheric Administration, University of California, Davis: Rachel Johnson The Nature Conservancy: Jeanette Howard and Julie Zimmerman State Water Resources Control Board: Chris Carr and Daniel Worth Trout Unlimited: Rene Henery University of California, Davis, San Francisco Public Utilities Commission: Ron Yoshiyama U.S. Bureau of Reclamation: Joshua Israel U.S. Fish and Wildlife Service: Paul Cadrett, Ramon Martin, and J.D. Wikert Prepared by Anchor QEA, LLC 1201 3rd Avenue, Suite 2600 Seattle, Washington 98101 April 2019 TABLE OF CONTENTS EXECUTIVE SUMMARY .........................................................................................................ES-I TECHNICAL SUMMARY .......................................................................................................TS-1 Foreword ......................................................................................................................................................................... 1 Introductio n ................................................................................................................................................................... 1 Purpose............................................................................................................................................................................ 5 Approach and Scope ................................................................................................................................................... 5 Policy Scope .............................................................................................................................................................. 6 Biological Scope....................................................................................................................................................... 6 Geographic Scope ................................................................................................................................................... 7 Logic Chain ..................................................................................................................................................................... 8 Structured and Collaborative Approach to Decision Making........................................................................ 11 Goals and Objectives ................................................................................................................................................. 13 Central Valley .......................................................................................................................................................... 13 Stanislaus River....................................................................................................................................................... 15 Biological Objectives ................................................................................................................................................. 15 Productivity ............................................................................................................................................................. 16 Life History Diversity ............................................................................................................................................. 21 Genetic Diversity .................................................................................................................................................... 26 Abundance .............................................................................................................................................................. 26 Environmental Objectives ........................................................................................................................................ 31 Stressors ........................................................................................................................................................................ 32 Stressor Identification, Ranking, and Prioritization...................................................................................... 32 Results of Stressor Analysis ................................................................................................................................ 34 Addressing Uncertainty ............................................................................................................................................ 38 Next Steps for the Stanislaus River ....................................................................................................................... 39 Beyond the Stanislaus River .................................................................................................................................... 40 1 INTRODUCTION .................................................................................................................1 2 SCOPE, CONTEXT, AND CONSIDERATIONS .........................................................................4 2.1 Historical Context ........................................................................................................................................... 4 2.2 Considerations for Biological and Environmental Objectives ........................................................... 5 2.3 Scope.................................................................................................................................................................. 6 2.3.1 Policy Considerations ............................................................................................................................. 6 2.3.2 Geographical Considerations............................................................................................................. 10 2.3.3 Biological Considerations.................................................................................................................... 12 2.4 Developing Foundational Elements Necessary for Conservation Planning (“Logic Chain”)... 13 Conservation Planning Foundation for Restoring April 2019 Chinook Salmon and O. mykiss in Stanislaus River i Table of Contents 3 VIABLE SALMONID POPULATION ATTRIBUTES ................................................................. 20 3.1 Abundance ..................................................................................................................................................... 20 3.2 Life History and Genetic Diversity............................................................................................................ 21 3.3 Productivity .................................................................................................................................................... 23 3.4 Spatial Structure............................................................................................................................................ 24 4 CURRENT STATUS OF CHINOOK SALMON AND O. MYKISS IN THE SAN JOAQUIN RIVER BASIN .................................................................................................................................... 26 4.1 Fall-run Chinook Salmon............................................................................................................................ 26 4.2 Spring-run Chinook Salmon...................................................................................................................... 27 4.3 O. mykiss (Steelhead and Resident Rainbow Trout)........................................................................... 30 4.4 Late Fall-run Chinook Salmon................................................................................................................... 31 5 STANISLAUS WATERSHED DESCRIPTION.......................................................................... 32 6 DEVELOPMENT OF GOALS AND OBJECTIVES SPECIFIC TO THE STANISLAUS RIVER..........