Endangered Species Act Section 7(a)(2) Consultation Biological Opinion & Magnuson-Stevens Fishery Conservation & Management Act Essential Fish Habitat Consultation Consultation on the "Willamette River Basin Flood Control Project" Action Agencies: u.s. Army Corps of Engineers Bonneville Power Administration U.S. Bureau of Reclamation Consultation Conducted by: NOAA's National Marine Fisheries Service (NMFS) Northwest Region NOAA Fisheries Log Number: FINWRl2000/02117 Date Issued: July 11, 2008 Issued by: D. Robert Lohn Regional Administrator NMFS Willamette Project Biological Opinion Table of Contents 1 INTRODUCTION 1.1 OBJECTIVES 1.2 CONSULTATION PROCEDURAL HISTORY 1.2.1 ESA Consultation on Willamette Project Operations 1.2.2 ESA Consultation on Willamette Project Hatcheries 1.2.3 Merging Hatcheries and Project Operations into a Single Consultation and Development of the 2007 Supplemental BA 1.2.4 Litigation and Settlement 1.3 CONSULTATION WITH AFFECTED INDIAN TRIBES 1.4 LISTED SPECIES OCCURRING WITHIN THE ACTION AREA 1.5 APPLICATION OF ESA SECTION 7(A)(2) STANDARDS – ANALYTICAL APPROACH 1.6 TERM OF THE OPINION 1.7 CONCLUSIONS 2 PROPOSED ACTION 2.1 GENERAL DESCRIPTION AND PURPOSES OF THE WILLAMETTE PROJECT 2.2 WILLAMETTE PROJECT ADMINISTRATION, ROLES OF USACE, BPA, RECLAMATION 2.2.1 US Army Corps of Engineers’ Roles 2.2.2 US Bureau of Reclamation’s Roles 2.2.3 Bonneville Power Administration’s Roles 2.3 PROJECT PURPOSES AND RESPONSIBILITIES 2.3.1 Flood Control 2.3.2 Irrigation Water Supply 2.3.3 Municipal and Industrial Water Supply 2.3.4 Navigation 2.3.5 Flow Augmentation 2.3.6 Hydroelectric Power Generation 2.3.7 Recreation 2.3.8 System Operation 2.3.9 Land Use Management 2.3.10 Bank Protection Program 2.3.11 Emergency Assistance Program 2.3.12 Fish Conservation 2.4 THE 2007 SUPPLEMENTAL BIOLOGICAL ASSESSMENT 2.5 TERM OF PROPOSED ACTION 2.6 CONTINUING COORDINATION AND MANAGEMENT 2.6.1 Federal Agency Manager’s Forum 2.6.2 WATER Steering Committee 2.6.3 WATER Technical Coordinating Committees 2.6.4 Flow Management Committee 2.6.5 Fish Passage and Hatchery Management Committee 2.6.6 Construction Projects Environmental Coordinating Committee 2.6.7 Water Quality/Temperature Control Committee 2.7 PROJECT PLANS 2.7.1 Routine and Non-routine Operations and Maintenance Activities 2.7.2 Willamette Fish Passage and Management Plan 2.8 FLOW MANAGEMENT MEASURES 2.8.1 WATER Flow Management Committee Table of Contents i July 11, 2008 NMFS Willamette Project Biological Opinion 2.8.2 Protocol for Notification of Deviations 2.8.3 Minimum Mainstem Flows 2.8.4 Minimum and Maximum Tributary Flows 2.8.5 Ramping Rates 2.8.6 Foster Dam Spring Spill 2.8.7 Flow-related Research, Monitoring and Evaluation (RM&E) 2.9 BUREAU OF RECLAMATION WATER MARKETING PROGRAM 2.10 FISH HATCHERIES AND RELATED PROGRAMS 2.10.1 Spring Chinook Reintroduction/Outplant Program 2.10.2 North Santiam Spring Chinook Hatchery Program 2.10.3 South Santiam Spring Chinook Hatchery Program 2.10.4 McKenzie Spring Chinook Program 2.10.5 Middle Fork Willamette Spring Chinook Hatchery Program 2.10.6 Upper Willamette Summer Steelhead Hatchery Program 2.10.7 Rainbow Trout Mitigation Program 2.10.8 Hatchery Mitigation Program Research, Monitoring and Evaluation 2.11 HABITAT RESTORATION AND MANAGEMENT ACTIONS 2.11.1 Onsite Habitat Restoration and Resource Stewardship Actions 2.11.2 Offsite Habitat Restoration Actions 2.11.3 North Santiam Gravel and Large Wood Restoration Study 2.11.4 Willamette River Bank Protection Program 2.11.5 Habitat-Related Research Monitoring and Evaluation 2.12 STRUCTURAL MODIFICATIONS: FISH PASSAGE, TEMPERATURE CONTROL AND HATCHERIES 2.12.1 Cougar Dam Adult Fish Collection Facility and RME Program 2.12.2 Willamette Valley Fish Handling and Transport Facilities Improvements 2.12.3 Willamette System Review Study 2.12.4 Construction Projects Environmental Coordination and Management 2.12.5 Conceptual Implementation Schedule 2.13 WATER QUALITY ACTIONS 2.13.1 Cougar Dam Temperature Control Project 2.13.2 TMDL Water Quality Management Plan 2.13.3 Water Quality Research Monitoring & Evaluation 2.14 RESEARCH, MONITORING AND EVALUATION PROGRAM 2.14.1 Coordination with the FCRPS RME Plan 2.14.2 Guiding Principles and Strategic Questions for RM&E Needs 2.15 DESCRIPTION OF THE ACTION AREA 3 RANGEWIDE STATUS 3.1 RANGEWIDE STATUS OF THE SPECIES 3.2 LIFE HISTORIES, FACTORS FOR DECLINE, AND POPULATION TRENDS 3.2.1 Upper Willamette River Chinook Salmon 3.2.2 Upper Willamette River Steelhead 3.2.3 Lower Columbia River Salmon and Steelhead Species 3.2.4 Interior Columbia River ESU/DPSs 3.3 CRITICAL HABITAT FOR COLUMBIA AND WILLAMETTE BASIN SALMONIDS 3.3.1 Critical Habitat for Upper Willamette River Chinook Salmon 3.3.2 Critical Habitat for Upper Willamette River Steelhead 3.3.3 Critical Habitat for Other ESU/DPSs Table of Contents ii July 11, 2008 NMFS Willamette Project Biological Opinion 4 ENVIRONMENTAL BASELINE 4.1 GENERAL BASELINE PERSPECTIVE 4.1.1 Project Effects in the Environmental Baseline 4.1.2 Large-scale Environmental Variation 4.1.3 Water Diversions 4.2 MIDDLE FORK WILLAMETTE 4.2.1 Historical Populations of Anadromous Salmonids in the Middle Fork Subbasin 4.2.2 Current Status of Anadromous Salmonids within the Middle Fork Willamette Subbasin 4.2.3 Environmental Conditions 4.2.4 Hatchery Programs 4.2.5 Fisheries 4.2.6 Status of PCEs of Designated Critical Habitat in the Middle Fork Willamette Subbasin 4.3 MCKENZIE SUBBASIN 4.3.1 Historical Populations of Anadromous Salmonids in the McKenzie Subbasin 4.3.2 Current Status of ESA-Listed Anadromous Salmonids within the Subbasin 4.3.3 Environmental Conditions 4.3.4 Hatchery Programs 4.3.5 Fisheries 4.3.6 Status of PCEs of Designated Critical Habitat in the McKenzie Subbasin 4.4 CALAPOOIA 4.4.1 Historical Populations of Anadromous Salmonids in the Calapooia Subbasin 4.4.2 Current Status of Anadromous Salmonids within the Calapooia Subbasin 4.4.3 Structures Impeding Fish Passage 4.4.4 Hatchery Program 4.4.5 Fisheries 4.4.6 Status of PCEs of Designated Critical Habitat and Factors Affecting those PCEs in the Calapooia River Subbasin 4.5 SOUTH SANTIAM SUBBASIN 4.5.1 Historical Populations of Anadromous Fish in the South Santiam Subbasin 4.5.2 Current Status of ESA-Listed Salmon and Steelhead within the Subbasin 4.5.3 Environmental Conditions 4.5.4 Hatchery Programs 4.5.5 Fisheries 4.5.6 Status of PCEs of Designated Critical Habitat in the South Santiam Subbasin 4.6 NORTH SANTIAM SUBBASIN 4.6.1 Historical Populations of Anadromous Salmonids in the Subbasin 4.6.2 Current Status of Native Anadromous Salmonids within the Subbasin 4.6.3 Environmental Conditions 4.6.4 Hatchery Programs 4.6.5 Fisheries 4.6.6 Status of PCEs of Designated Critical Habitat and Factors Affecting those PCEs in the North Santiam Subbasin 4.7 MOLALLA BASELINE 4.7.1 Historical Populations of Anadromous Salmonids 4.7.2 Current Status 4.7.3 Environmental Conditions 4.7.4 Hatchery Programs 4.7.5 Fisheries 4.7.6 Habitat Alteration 4.8 CLACKAMAS SUBBASIN 4.8.1 Historical Populations of Anadromous Salmonids in the Clackamas Subbasin Table of Contents iii July 11, 2008 NMFS Willamette Project Biological Opinion 4.8.2 Current status of ESA-Listed Salmon and Steelhead in the Subbasin 4.8.3 Environmental Conditions 4.8.4 Hatchery Programs 4.8.5 Harvest 4.8.6 Status of PCEs of Designated Critical Habitat in the Clackamas Subbasin 4.9 COAST FORK AND LONG TOM SUBBASINS 4.9.1 Historical Status of Anadromous Salmonids in the Coast Fork Willamette and Long Tom Subbasins 4.9.2 Current Status of Anadromous Salmonids in the Coast Fork and Long Tom Subbasins 4.9.3 Environmental Conditions 4.9.4 Hatchery Programs 4.9.5 Fisheries 4.9.6 Status of Habitat in the Coast Fork Willamette and Long Tom Subbasins 4.10 MAINSTEM WILLAMETTE 4.10.1 Historical Populations of Anadromous Salmonids in the Mainstem 4.10.2 Current Status of Native Anadromous Salmonids in the Mainstem 4.10.3 Environmental Conditions 4.10.4 Hatchery Programs 4.10.5 Fisheries 4.10.6 Status of PCEs of Designated Critical Habitat and Factors Affecting PCEs along the Mainstem Willamette 4.11 LOWER COLUMBIA RIVER, ESTUARY, PLUME, AND COASTAL OCEAN 4.11.1 Status of Habitat in the Lower Columbia River, Estuary, and Coastal Ocean 4.11.2 Hatchery Effects 4.11.3 Fisheries 4.11.4 Status of Designated Critical Habitat in the Lower Columbia River and Estuary 5 EFFECTS OF THE PROPOSED ACTION 5.1 EFFECTS OF THE PROPOSED ACTION COMMON TO MULTIPLE AREAS 5.1.1 WATER Committee Process and Structure 5.1.2 Willamette System Review Study 5.1.3 RME Studies 5.1.4 Revetments 5.1.5 General Effects of Hatchery Programs on ESA-listed Salmon and Steelhead 5.1.6 Water Marketing 5.1.7 Climate Change Considerations 5.2 MIDDLE FORK WILLAMETTE RIVER SUBBASIN 5.2.1 Habitat Access and Fish Passage 5.2.2 Water Quantity/Hydrograph 5.2.3 Water Quality 5.2.4 Physical Habitat Quality 5.2.5 Hatcheries 5.2.6 Summary of Effects on the Middle Fork Willamette Chinook Salmon Population 5.2.7 Effects of the Proposed Action on Designated Critical Habitat 5.3 MCKENZIE RIVER SUBBASIN 5.3.1 Habitat Access and Fish Passage 5.3.2 Water Quantity/Hydrograph 5.3.3 Water Quality 5.3.4 Physical Habitat Quality 5.3.5 Hatcheries 5.3.6 Summary of Effects on the McKenzie Chinook Salmon Population Table of Contents iv July 11, 2008 NMFS Willamette Project Biological Opinion 5.3.7 Effects of the Proposed Action on Designated Critical Habitat 5.4 CALAPOOIA SUBBASIN 5.4.1 Habitat Access and Fish Passage 5.4.2 Water Quantity/Hydrograph 5.4.3 Water Quality 5.4.4 Physical Habitat