Biological Assessment for Bureau of Reclamation Operations and Maintenance in the Snake River Basin above Brownlee Reservoir on Snake River Physa Snail (Haitia [Physa] natricina) U.S. Department of the Interior Bureau of Reclamation Pacific Northwest Region Snake River Area Office Boise, Idaho September 2014 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 for Bureau of Reclamation Operations and Maintenance in the Snake River Basin above Brownlee Reservoir on Snake River physa snail (Haitia [Physa] natricina) U.S. Department of the Interior Bureau of Reclamation Pacific Northwest Region Snake River Area Office Boise, Idaho September 2014 Acronyms and Abbreviations ADCP Acoustic Doppler Current Profile BA Biological Assessment BCSD Bias Correction Spatial Disaggregation BID Burley Irrigation District BiOp Biological Opinion BPA Bonneville Power Administration CFR Code of Federal Regulations cfs cubic feet per second Corps U.S. Army Corps of Engineers CWA Clean Water Act EA Environmental Assessment EFH essential fish habitat EIS Environmental Impact Statement EPA Environmental Protection Agency ESA Endangered Species Act FERC Federal Energy Regulatory Commission FONSI Finding of No Significant Impact FR Federal Register GCM global climate (circulation) model IDEQ Idaho Department of Environmental Quality ITS Incidental Take Statement LW/D less warming and drier LW/W less warming and wetter MC minimal change MID Minidoka Irrigation District MW megawatt MW/D more warming and drier MW/W more warming and wetter NEPA National Environmental Policy Act NOAA Fisheries National Oceanic and Atmospheric Administration National Marine Fisheries Service O&M operation and maintenance Reclamation U.S. Bureau of Reclamation RM river mile RMJOC River Management Joint Operating Committee ROD Record of Decision SCADA Supervisory Control and Data Acquisition Term Sheet Nez Perce Term Sheet TMDL Total Maximum Daily Load TP Total Phosphorus TSS Total Suspended Solids USFWS U.S. Fish and Wildlife Service USGS U.S. Geological Survey UWCIG University of Washington Climate Impact Group CONTENTS Acronyms and Abbreviations Chapter 1 Overview ........................................................................................ 1 1.1 Purpose of the Biological Assessment .................................................................... 1 1.2 Background and Consultation History .................................................................... 3 1.2.1 Relationship to Existing Biological Opinions............................................. 3 1.3 Proposed Actions .................................................................................................... 4 1.4 Action Area ............................................................................................................. 5 1.5 Duration of the Proposed Action ............................................................................ 9 1.6 Effect Determinations for Snake River physa ........................................................ 9 1.7 How to Read This Document ................................................................................ 10 Chapter 2 Description of the Proposed Action ............................................. 13 2.1 Introduction ........................................................................................................... 13 2.2 Current System Management ................................................................................ 13 2.2.1 Overview ................................................................................................... 13 2.3 Future O&M in the Snake River System above Milner Dam ............................... 17 2.3.1 The New Spillway..................................................................................... 18 2.3.2 Operation of Spillway ............................................................................... 18 2.3.3 Adaptive Management .............................................................................. 23 2.3.4 Interagency Technical Team ..................................................................... 24 2.3.5 Summary of Proposed Snake River Operations above Milner Dam ........ 26 2.4 Future O&M in the Snake River above Brownlee Reservoir ............................... 26 2.5 Future Provision of Salmon Flow Augmentation ................................................. 27 2.6 Snake River System Maintenance Activities ........................................................ 27 Chapter 3 Hydrologic and Water Quality Conditions ................................... 29 3.1 Upper Snake River Current Hydrologic Conditions ............................................. 29 3.1.1 Hydrologic Data Analysis Background .................................................... 29 3.1.2 Snake River above Milner Dam ................................................................ 31 3.1.3 Minidoka Dam Spillway ........................................................................... 32 Spillway Construction History .................................................................. 32 Current Conditions .................................................................................... 33 3.1.4 Snake River above Brownlee Reservoir ................................................... 35 September 2014 – Final i CONTENTS (CONTINUED) 3.1.5 Flow Augmentation .................................................................................. 40 3.2 Future Hydrologic Conditions .............................................................................. 41 3.2.1 MODSIM-DSS Water Resource Model ................................................... 43 3.2.2 Analysis from the RMJOC Climate Change Study .................................. 44 3.3 Possible Effects of Future Climate Change .......................................................... 49 3.4 Current Upper Snake River Water Quality Conditions ........................................ 50 3.5 Minidoka Dam Spillway Water Quality Conditions ............................................. 52 3.5.1 Current Conditions .................................................................................... 52 3.5.2 Adaptive Management Spillway Release Analysis .................................. 64 Chapter 4 Snake River Physa Analysis ......................................................... 67 4.1 Introduction ........................................................................................................... 67 4.2 Background ........................................................................................................... 67 4.2.1 Snake River Physa and Action Area ......................................................... 67 4.2.2 Species Description and Needs ................................................................. 68 4.3 Effects of the Proposed Action ............................................................................. 70 Minidoka Dam Spillway ........................................................................... 70 Snake River from Minidoka Dam Downstream to I-84 Bridge ................ 78 Snake River from Milner Dam Downstream to Brownlee Reservoir ....... 84 4.4 Cumulative Effects................................................................................................ 87 4.5 Effects Conclusion ................................................................................................ 87 Chapter 5 References ................................................................................... 89 List of Figures Figure 1-1. Minidoka BA project area. ...................................................................................... 2 Figure 1-2. Reclamation’s Snake River physa Segment 1 analysis area (11.6-mile reach starting at Minidoka Dam and extending downstream to the I-84 Bridge). ........... 6 Figure 1-3. Reclamation’s Snake River physa Segment 2 analysis area (spillway area located below Minidoka Dam)................................................................................ 7 Figure 1-4. Reclamation’s Snake River physa Segment 3 analysis area (Snake River from Milner Dam downstream to above Brownlee Reservoir). ...................................... 8 Figure 2-1. Reclamation facilities located in the upper Snake River basin. ............................ 15 ii September 2014 – Final CONTENTS (CONTINUED) Figure 2-2. Comparison of average outflow from Minidoka and American Falls dams. Note how Minidoka Dam outflow matches American Fall Dam outflow. The reduction in outflow from Minidoka Dam relative to American Falls Dam from April 1 through October 1 is due to diversions into the Northside and Southside canals located at Minidoka Dam. ......................................................... 17 Figure 2-3. Minidoka Dam spillway release points. ................................................................ 21 Figure 3-1. Summary hydrograph for flows below Minidoka Dam. ....................................... 31 Figure 3-2. Summary hydrograph for flows below Milner Dam............................................. 32 Figure 3-3. Summary