LIST OF ABBREVIATIONS AND ACRONYMS BMPs Best Management Practices BA Biological Assessment BO Biological Opinion CCV California Central Valley CDFG California Department of Fish and Game CDFW California Department of Fish and Wildlife DWR California Department of Water Resources CV Central Valley CVI Central Valley Index TRT Central Valley Technical Review Team CWT Coded-wire tag CRR Cohort Replacement Rates Coleman Coleman National Fish Hatchery DO Dissolved Oxygen DPS Distinct Population Segment EBMUD East Bay Municipal Utilities District ESA Endangered Species Act EFH Essential Fish Habitat ESU Evolutionarily Significant Unit FRFH Feather River Fish Hatchery FRRP Fish Rescue and Relocation Plan GIS Geographic Information System LWM Large Woody Material MSA Magnuson-Stevens Fishery Conservation and Management Act MMP Monitoring and Maintenance Plan NMFS National Marine Fisheries Service NOAA National Oceanic and Atmospheric Administration NEP Non-essential Experimental Population PFMC Pacific Fishery Management Council PBFs Physical or Biological Features PVA Population Viability Analysis RBDD Red Bluff Diversion Dam RM River Mile RST Rotary Screw Trap SJR San Joaquin River SJRRP San Joaquin River Restoration Program T&C Terms and Conditions DQA The Data Quality Act Corps U.S. Army Corps of Engineers Reclamation U.S. Bureau of Reclamation USFWS U.S. Fish and Wildlife Service VSP Viable Salmonid Population 2 TABLE OF CONTENTS 1. INTRODUCTION .............................................................................................................. 5 1.1 Background, Authority, and Policy ............................................................................... 5 1.2 Consultation History ....................................................................................................... 6 1.3 Proposed Action .............................................................................................................. 7 1.3.1 Columbia Canal Intake and Siphon ............................................................................... 8 1.3.2 Compact Bypass, Compact Bypass Control Structure, and Mendota Pool Control Structure ................................................................................................................................ 11 1.3.3 Reach 2B Grading, Levees, and Floodplain Project Descriptions ............................... 17 1.3.4 Fish Passage Facility on the San Joaquin River Control Structure at the Chowchilla Bifurcation Structure ............................................................................................................. 34 1.3.5 Mendota Pool Control Structure Fish Screen .............................................................. 37 1.3.6 Conservation Measures and Avoidance/Minimization Measures ................................ 38 1.4 Action Area .................................................................................................................... 40 2. ENDANGERED SPECIES ACT: .................................................................................... 42 2.1 Analytical Approach ..................................................................................................... 42 2.2 Range-wide Status of the Species................................................................................. 43 2.2.2 California Central Valley Steelhead distinct population segment (DPS) .................... 43 2.2.1 Central Valley spring-run Chinook salmon Evolutionarily Significant Unit (ESU) ... 59 2.2.3 Climate Change ............................................................................................................ 75 2.3 Environmental Baseline ............................................................................................... 77 2.3.1 Status of the Species in the Action Area ...................................................................... 77 2.3.2 Factors Affecting the Species in the Action Area ........................................................ 81 2.3.3 NMFS’ Salmon and Steelhead Recovery Plan Action Recommendations .................. 83 2.3.4 Climate Change ............................................................................................................ 83 2.4 Effects of the Action ...................................................................................................... 83 2.4.1 Construction and Maintenance Effects ........................................................................ 85 2.4.1.1 Erosion and Sedimentation ....................................................................................... 86 2.4.1.2 Increased Turbidity ................................................................................................... 86 2.4.1.3 Loss/Degradation of Habitat ..................................................................................... 87 2.4.1.4 Hazardous Materials ................................................................................................. 87 2.4.1.5 Increased Temperature .............................................................................................. 87 2.4.1.6 Hazardous Noise Levels ........................................................................................... 88 2.4.2 Operational Effects ...................................................................................................... 89 2.4.3 Beneficial Effects ......................................................................................................... 93 2.5 Cumulative Effects ........................................................................................................ 95 2.6 Integration and Synthesis ............................................................................................. 96 2.6.1 Status of the Species and Effects of the action on listed species ................................. 96 2.6.2 Summary ...................................................................................................................... 98 2.7 Conclusion ..................................................................................................................... 98 2.8 Incidental Take Statement ........................................................................................... 99 2.8.1 Amount or Extent of Take ........................................................................................... 99 2.8.2 Effect of the Take....................................................................................................... 101 2.8.3 Reasonable and Prudent Measures ............................................................................. 101 2.8.4 Terms and Conditions ................................................................................................ 102 2.9 Conservation Recommendations ............................................................................... 106 3 2.10 Reinitiation of Consultation ..................................................................................... 107 3. MAGNUSON-STEVENS FISHERY CONSERVATION AND MANAGEMENT ACT ESSENTIAL FISH HABITAT CONSULTATION ........................................................... 108 3.1 Essential Fish Habitat Affected by the Proposed Action ........................................ 108 3.1.1 Life History ................................................................................................................ 109 3.1.2 Habitat Areas of Particular Concern .......................................................................... 110 3.2 Adverse Effects on Essential Fish Habitat ................................................................ 110 3.3 Essential Fish Habitat Conservation Recommendations ........................................ 111 3.4 Statutory Response Requirement .............................................................................. 113 3.5 Supplemental Consultation ........................................................................................ 114 4. FISH AND WILDLIFE COORDINATION ACT .......................................................... 114 5. DATA QUALITY ACT DOCUMENTATION AND PRE-DISSEMINATION REVIEW ............................................................................................................................. 115 5.1 Utility ............................................................................................................ 115 5.2 Integrity ....................................................................................................... 115 5.3 Objectivity ................................................................................................... 115 FEDERAL REGISTER NOTICES CITED ........................................................................ 116 LITERATURE CITED ....................................................................................................... 117 4 1. INTRODUCTION 1.1 Background, Authority, and Policy The National Marine Fisheries Service (NMFS) prepared the biological opinion (BO) and incidental take statement portions (ITS) of this document in accordance with section 7(b) of the Endangered Species Act (ESA) of 1973 (16 USC 1531 et seq.), and implementing regulations at 50 CFR 402. We also completed an EFH consultation on the proposed action, in accordance with section 305(b)(2) of the Magnuson-Stevens Fishery Conservation and Management Act (MSA) (16 U.S.C. 1801 et seq.) and implementing regulations at 50 CFR 600. Because the proposed action would modify a stream or other body of water, NMFS also provides