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Biological Assessment on the Future Operation and Maintenance of the Rogue River Basin Project

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Biological Assessment on the Future Operation and Maintenance of the Rogue River Basin Project Biological Assessment on the Future Operation and Maintenance of the Rogue River Basin Project Talent Division U.S. Department of the Interior Bureau of Reclamation Pacific Northwest Region Columbia-Cascades Area Office, Yakima, Washington Pacific Northwest Regional Office, Boise, Idaho October 2009 U.S. DEPARTMENT OF THE INTERIOR The mission of the Department of the Interior is to protect and provide access to our Nation’s natural and cultural heritage and honor our trust responsibilities to Indian tribes and our commitments to island communities. MISSION OF THE BUREAU OF RECLAMATION The mission of the Bureau of Reclamation is to manage, develop, and protect water and related resources in an environmentally and economically sound manner in the interest of the American public. Biological Assessment on the Future Operation and Maintenance of the Rogue River Basin Project Talent Division U.S. Department of the Interior Bureau of Reclamation Pacific Northwest Region Columbia-Cascades Area Office, Yakima, Washington Pacific Northwest Regional Office, Boise, Idaho October 2009 Acronyms and Abbreviations BA Biological Assessment BiOp Biological Opinion BCWC Bear Creek Watershed Council BLM Bureau of Land Management BMP Best management practices BRT West Coast Coho Salmon Biological Review Team cfs Cubic feet per second CIG Climate Impacts Group, University of Washington Corps U.S. Army Corps of Engineers CWA Clean Water Act DPS Distinct population segment EFH Essential fish habitat EPA Environmental Protection Agency ESA Endangered Species Act ESU Evolutionarily Significant Unit FR Federal Register HUC Hydrologic Unit Code IFIM Instream Flow Incremental Methodology IPOD Irrigation point of diversion LWD Large woody debris MBI Migratory Barrier Index MID Medford Irrigation District MSA Magnuson-Stevens Fishery Conservation and Management Act NCCSP National Center for Conservation Science and Policy NEPA National Environmental Policy Act NOAA Fisheries National Oceanic and Atmospheric Administration, National Marine Fisheries Service (also known as NMFS) NPDES National Pollution Discharge Elimination System O&M operations and maintenance ODEQ Oregon Department of Environmental Quality ODFW Oregon Department of Fish and Wildlife OWEB Oregon Watershed Enhancement Board OWRD Oregon Water Resources Department PCE Primary constituent element PHABSIM Physical Habitat Simulation System RBFATT Rogue Basin Fish Access Technical Team Reclamation U.S. Bureau of Reclamation RM River mile RRVID Rogue River Valley Irrigation District RPA Reasonable and prudent alternative RVCOG Rogue Valley Council of Governments SMU Species management unit SONCC Southern Oregon/Northern California Coast Coho TID Talent Irrigation District TMDL Total Maximum Daily Load TRT Technical Review Team USFS U.S. Forest Service USFWS U.S. Fish and Wildlife Service VSP viable salmonid population WISE Water for Irrigation, Streams, and the Economy WUA Weighted usable area TABLE OF CONTENTS Acronyms and Abbreviations Table of Contents.............................................................................................. i Chapter 1 Introduction.................................................................................. 1 1.1 Purpose .................................................................................................................... 1 1.2 History of the Rogue Project Section 7 ESA Consultation..................................... 5 1.2.1 Previous Consultations................................................................................ 5 1.2.2 Coordination in the Preparation of the Biological Assessment.................................................................................................. 5 1.3 Proposed Action ...................................................................................................... 8 1.4 Action Area ........................................................................................................... 11 1.5 Listed Species in the Action Area ......................................................................... 12 Chapter 2 Rogue River Project Facilities ..................................................... 13 2.1 Upper South Fork Little Butte Creek Area and Bear Creek Area......................... 13 2.1.1 Water Collection and Storage Facilities.................................................... 14 2.2 Antelope Creek/Dry Creek Areas.......................................................................... 20 2.2.1 Water Collection and Storage Facilities.................................................... 21 2.3 Maintenance .......................................................................................................... 21 2.3.1 Inspection.................................................................................................. 22 2.3.2 Routine Maintenance ................................................................................ 22 2.3.3 Green Springs Powerplant ........................................................................ 23 Chapter 3 Environmental Baseline .............................................................. 25 3.1 Fisheries................................................................................................................. 25 3.1.1 Current Range-wide Status of the SONCC Coho Salmon........................ 25 3.1.2 Current Status of Upper Rogue River Subbasin Independent Population ................................................................................................. 28 3.1.3 Current Conservation Efforts.................................................................... 45 3.2 Hydrology.............................................................................................................. 48 3.2.1 Bear Creek Watershed .............................................................................. 53 3.2.2 Little Butte Creek Watershed.................................................................... 63 3.2.3 Klamath River Basin................................................................................. 69 October 2009 – Rogue River Project Biological Assessment i 3.3 Habitat Conditions .................................................................................................69 3.3.1 Bear Creek Watershed ...............................................................................69 3.3.2 Little Butte Creek Watershed ....................................................................82 3.3.3 Klamath River Basin..................................................................................93 3.4 Critical Habitat for the SONCC Coho Salmon ......................................................97 Chapter 4 Proposed Action.......................................................................... 99 4.1 Description .............................................................................................................99 4.1.1 Ramping Rates at Emigrant Dam ............................................................101 4.1.2 Minimum Operational Releases for Emigrant Creek ..............................102 4.1.3 Gaging Station .........................................................................................107 4.1.4 Fish Passage Improvement ......................................................................107 4.2 Interrelated and Interdependent Actions ..............................................................113 Chapter 5 Effects of the Action ................................................................. 115 5.1 Effects to Hydrology............................................................................................115 5.1.1 Bear Creek Watershed .............................................................................116 5.1.2 Little Butte Creek and Antelope Creek Watersheds................................120 5.1.3 Klamath River Basin................................................................................121 5.2 Effects to SONCC Coho Salmon Critical Habitat ...............................................121 5.2.1 Bear Creek Watershed .............................................................................122 5.2.2 Little Butte Creek Watershed ..................................................................152 5.2.3 Klamath River Watershed........................................................................160 5.2.4 Summary..................................................................................................161 5.3 Effects to SONCC Coho Salmon .........................................................................162 5.3.1 Factors Affecting Juvenile Coho Salmon ................................................167 5.4 Effects Determination ..........................................................................................172 Chapter 6 Cumulative Effects.................................................................... 175 6.1 Water Conservation Efforts..................................................................................175 6.2 Fish Passage Improvements .................................................................................176 6.3 Population Growth and Associated Development ...............................................176 6.4 Climate Change....................................................................................................176 6.5 Klamath Basin......................................................................................................178 Chapter 7 Bibliography 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