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Biological Assessment for Bull Trout Critical Habitat in the Upper Snake River Basin

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Biological Assessment for Bull Trout Critical Habitat in the Upper Snake River Basin Biological Assessment for Bull Trout Critical Habitat in the Upper Snake River Basin U.S. Department of the Interior Bureau of Reclamation Pacific Northwest Regional Office Snake River Area Office Boise, Idaho December 2013 MISSION OF THE U.S. DEPARTMENT OF THE INTERIOR PROTECTING AMERICA'S GREAT OUTDOORS AND POWERING OUR FUTURE The U.S. Department of the Interior protects America’s natural resources and heritage, honors our cultures and tribal communities, and supplies the energy to power our future. 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. Photograph on front cover: Aerial view of Mason Dam and Phillips Lake, Oregon, Upper Division, Baker Project, Oregon. Biological Assessment for Bull Trout Critical Habitat in the Upper Snake River Basin U.S. Department of the Interior Bureau of Reclamation Pacific Northwest Regional Office Snake River Area Office Boise, Idaho December 2013 This page intentionally left blank. Acronyms and Abbreviations °C degrees Celsius 2004 Operations Operation Description of Bureau of Reclamation Projects in the Snake River Above Brownlee Reservoir 2004 Upper Snake BA Biological Assessment for Bureau of Reclamation Operations and Maintenance in the Snake River Basin above Brownlee Reservoir 2004/2007 Upper Snake BA 2004 Upper Snake Biological Assessment as amended by the 2007 Upper Snake Biological Assessment 2005 USFWS BiOp U.S. Fish and Wildlife Service Biological Opinion for Bureau of Reclamation Operations and Maintenance in the Snake River Basin above Brownlee Reservoir 2007 Upper Snake BA Biological Assessment for Bureau of Reclamation Operation and Maintenance in the Upper Snake River Basin above Brownlee Reservoir 2008 NOAA Fisheries BiOp NOAA Fisheries Service Biological Opinion Consultation for the Operation and Maintenance of 10 U.S. Bureau of Reclamation Projects and 2 Related Action in the Upper Snake River Basin above Brownlee Reservoir BA biological assessment BiOp biological opinion cfs cubic feet per second CHSU critical habitat subunit CHU critical habitat unit Corps of Engineers U.S. Army Corps of Engineers Draft Recovery Plan Bull Trout Draft Recovery Plan (2002) EOM end of month ESA Endangered Species Act FCRPS Federal Columbia River Power System FMO foraging, migrating, and over-wintering habitat FY fiscal year HD Hybrid-Delta scenarios HD 2020s Hybrid-Delta scenario covering time period 2010 to 2039 IDEQ Idaho Department of Environmental Quality NOAA Fisheries Service National Oceanic and Atmospheric Administration, National Marine Fisheries Service O&M operation and maintenance ODEQ Oregon Department of Environmental Quality ODFW Oregon Department of Fish and Wildlife PCE primary constituent elements POR period of record Reclamation U.S. Department of the Interior, Bureau of Reclamation RMJOC River Management Joint Operating Committee RU recovery unit States States of Idaho and Oregon T&C terms and conditions TMDL Total Maximum Daily Load (planning process) TN:TP total nitrogen-to-total phosphorus ratio upper Snake River projects Reclamation projects in the Snake River basin above Brownlee Reservoir USFS U.S. Department of Agriculture, Forest Service USFWS U.S. Department of the Interior, Fish and Wildlife Service USGS U.S. Department of the Interior, Geological Survey UW CIG University of Washington Climate Impacts Group VIC variable infiltration capacity hydrologic model WY water year Table of Contents 1.0 Introduction .................................................................................................................... 1 1.1 How to Read this Document .............................................................................. 1 1.2 Background ........................................................................................................ 2 1.3 Proposed Actions ................................................................................................ 3 1.4 Action Areas ....................................................................................................... 4 1.5 Duration of Proposed Actions ............................................................................ 6 1.6 Summary of Determinations of Effects .............................................................. 6 1.6.1 Summary of Designated Critical Habitat Effects in the Action Areas .......................................................................................... 6 1.6.2 Summary of Bull Trout Effects in the Powder River System ................ 7 2.0 Overview of Hydrology and Water Quality in the Upper Snake River Basin ................................................................................................................................. 8 2.1 Hydrology ........................................................................................................... 8 2.1.1 Current Flow Conditions ........................................................................ 9 2.1.2 Historical Flow Conditions .................................................................. 10 2.2 Future Hydrologic Conditions/Climate Change ............................................... 10 2.2.1 Analysis from the RMJOC Climate Change Study ............................. 10 2.2.2 RMJOC Climate Change Study Modeled Climate Change Effects on Inflows ................................................................................ 13 2.2.3 RMJOC Modeled Climate Change Effects on End-of-Month Storage ................................................................................................. 13 2.2.4 RMJOC Climate Change Study Modeled Climate Change Effects on Flow .................................................................................... 14 2.2.5 RMJOC Climate Change Study Modeled Climate Change Effects Flow Augmentation for ESA-listed Species and Resident Fish ........................................................................................ 15 2.2.6 RMJOC Climate Change Study Modeled Climate Change Effects on Critical Habitat.................................................................... 16 2.2.7 RMJOC Climate Change Study Summary .......................................... 17 2.3 Water Quality ................................................................................................... 17 2.3.1 Total Maximum Daily Load (TMDL) ................................................. 17 December 2013 – Upper Snake River Bull Trout Critical Habitat Biological Assessment i 3.0 Overview of Bull Trout in the Upper Snake River Basin ......................................... 19 3.1 Critical Habitat Designations ........................................................................... 19 3.1.1 Locations of Critical Habitats in this Assessment ............................... 20 3.1.2 Upper Snake Recovery Unit ................................................................ 20 3.1.3 Mid-Columbia Recovery Unit ............................................................. 21 3.1.4 Coastal Recovery Unit ......................................................................... 21 3.1.5 Primary Constituent Elements ............................................................. 22 3.2 Recovery Planning ........................................................................................... 23 3.3 Critical Habitat Analyses in this Assessment................................................... 23 3.3.1 Analysis of PCEs in this Assessment .................................................. 24 4.0 Boise River System ....................................................................................................... 29 4.1 Proposed Action ............................................................................................... 29 4.2 Action Area ...................................................................................................... 32 4.3 Environmental Baseline ................................................................................... 35 4.3.1 Baseline Hydrology ............................................................................. 35 4.3.2 Baseline Population Status and Trends ................................................ 43 4.3.3 Baseline Critical Habitat Conditions ................................................... 44 4.4 Effects of the Proposed Actions ....................................................................... 58 4.4.1 Effects of the Proposed Action on Bull Trout ..................................... 58 4.4.2 Effects of the Proposed Action on Critical Habitat ............................. 59 4.4.3 Summary of the Effects of the Proposed Action on Critical Habitat .................................................................................................. 70 4.5 Cumulative Effects ........................................................................................... 72 4.6 Determination ................................................................................................... 72 5.0 Deadwood and South Fork Payette River System ..................................................... 74 5.1 Proposed Action ............................................................................................... 74 5.2 Action Area ...................................................................................................... 76 5.3 Environmental Baseline ..................................................................................
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