USFWS Final Biological Opinion on the Willamette River Basin Flood Control Project Endangered Species Act • Section 7 Consultation BIOLOGICAL OPINION On the Continued Operation and Maintenance ofthe Willamette River Basin Project and Effects to Oregon Chub, Bull Trout, and Bull Trout Critical Habitat Designated Under the Endangered Species Act. As Proposed by: u.S. Army Corps ofEngineers (Department ofArmy) Bonneville Power Administration (Department ofEnergy) • Bureau ofReclamation (Department ofInterior) Prepared by: u.S. Fish and Wildlife Service Oregon Fish and Wildlife Office File Number: 8330.F0224(07) Tails Number:13420-2007-F-0024 Approved by: Date: • Acting State Supervisor 1 July 11, 2008 USFWS Final Biological Opinion on the Willamette River Basin Flood Control Project This page has been intentionally left blank ___________________________________________________________________________ 2 July 11, 2008 USFWS Final Biological Opinion on the Willamette River Basin Flood Control Project Table of Contents 1. INTRODUCTION ..................................................................................................................... 9 1.1 Consultation History .......................................................................................................... 10 2. RELATED BIOLOGICAL OPINIONS .................................................................................. 15 2.1 Willamette Project Consultation on Effects to Oregon Chub............................................ 15 2.2 Cougar Dam Water Temperature Control Construction.................................................... 15 2.3 Cougar Dam Fish Collection Facility ................................................................................ 16 2.4 Carmen Smith Hydroelectric Project Interim Biological Opinion .................................... 16 2.5 Federal Columbia River Power System............................................................................. 16 2.6 Oregon Chub Spawning Habitat Enhancement at Hospital Pond...................................... 17 2.7 USACE Management Activities for Rare Plants and Insects at Fern Ridge Reservoir..... 17 3. CONCURRENCES.................................................................................................................. 19 3.1 Background........................................................................................................................ 19 3.2 Plant and Invertebrate Species........................................................................................... 19 3.3 Vertebrate Species ............................................................................................................. 20 3.3.1 Columbian White-Tailed Deer.................................................................................... 20 3.3.2 Bald Eagle................................................................................................................... 21 3.3.3 Northern Spotted Owl................................................................................................. 21 4. DESCRIPTION OF THE PROPOSED ACTION ................................................................... 22 4.1 General Description of Willamette Project Base Operations ............................................ 23 4.1.1 Willamette Project Development Timeline ................................................................ 23 4.1.2 Project Administration................................................................................................ 23 4.1.3 Fisheries Mitigation .................................................................................................... 24 4.1.4 System Operation........................................................................................................ 24 4.1.5 Land Use Management ............................................................................................... 25 4.1.6 Bank Protection Program............................................................................................ 25 4.1.7 Emergency Assistance Program ................................................................................. 28 4.1.8 Bureau of Reclamation Activities............................................................................... 28 4.1.9 Bonneville Power Administration Activities.............................................................. 30 4.2 Project Operations Described by Purpose.......................................................................... 31 4.2.1 Flood Control.............................................................................................................. 31 4.2.2 Irrigation ..................................................................................................................... 33 4.2.3 Municipal and Industrial Water Supply...................................................................... 34 4.2.4 Navigation................................................................................................................... 34 4.2.5 Flow Augmentation .................................................................................................... 35 4.2.6 Hydroelectric Power Generation................................................................................. 35 4.2.7 Recreation ................................................................................................................... 36 4.3 Willamette Project Authorizations..................................................................................... 37 5. REVISED PROPOSED ACTION WITH NMFS RPA INCORPORATED ........................... 38 5.1 Coordination ...................................................................................................................... 38 5.1.1 Charter of WATER..................................................................................................... 38 5.1.2 Technical Sub-Committees of WATER ..................................................................... 39 5.1.3 WATER Decision-Making Process ............................................................................ 39 5.1.4 Role of Services in Decision-Making (Agreement with Action Agencies)................ 40 ___________________________________________________________________________ 3 July 11, 2008 USFWS Final Biological Opinion on the Willamette River Basin Flood Control Project 5.2 Flow Management ............................................................................................................. 40 5.2.1 WATER Flow Management Committee .................................................................... 41 5.2.2 Protocol for Notification of Deviations ...................................................................... 42 5.2.3 Minimum Mainstem Flow Objectives ........................................................................ 42 5.2.4 Tributary Flow Objectives –Project Release Minimums............................................ 42 5.2.5 Tributary Flows –Project Release Maximums............................................................ 46 5.2.6 Ramping Rates............................................................................................................ 47 5.2.8 Foster Spring Spill ...................................................................................................... 51 5.2.9 Protecting Stored Water Released for Fish................................................................. 51 5.2.10 Flow Related Research, Monitoring and Evaluation ................................................ 51 5.3 Water Contract Program .................................................................................................... 52 5.3.1 Bureau of Reclamation Water Contract Program ....................................................... 52 5.3.2 New Contract Issuance ............................................................................................... 52 5.3.3 Existing Contracts....................................................................................................... 53 5.3.4 New and Renewed Contracts – Conditions ................................................................ 54 5.3.5 Annual Availability of Contract Water for Irrigation................................................. 54 5.4 Fish Passage....................................................................................................................... 55 5.4.1 Adult Chinook Salmon Outplanting ........................................................................... 56 5.4.2 Winter Steelhead Passage ........................................................................................... 56 5.4.3 Willamette Fish Operations Plan ................................................................................ 57 5.4.4 Annual Revision of Willamette Fish Operations Plan (WFOP) .................................. 58 5.4.5 Employee Training for Fish Protection Operations at Project Dams and Fish Facilities ............................................................................................................................................... 58 5.4.6 Upgrade Existing Adult Fish Collection and Handling Facilities .............................. 59 5.4.7 Adult Fish Release Sites Above Dams ....................................................................... 59 5.4.8 Interim Downstream Fish Passage through Reservoirs and Dams ............................. 60 5.4.9 Fall Creek Drawdown................................................................................................