U.S. Fish & Wildlife Service Final Biological Opinion
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Biological Opinion Endangered Species Act Section 7 Consultation U.S. Fish and Wildlife Service Loup River Hydroelectric Project Project No. P-1256-031 Agency: Federal Energy Regulatory Commission Consultation Conducted By: U.S. Fish and Wildlife Service Nebraska Ecological Services Field Office December 16, 2016 ____________________________ ___12/16/2016_________ Eliza Hines, Field Supervisor Date Nebraska Field Office Biological Opinion – Project No. 1256-031 TABLE OF CONTENTS I CONSULTATION HISTORY ................................................................................................ 1 II DESCRIPTION OF THE FEDERAL ACTION ..................................................................... 9 IIA Project Description, Location, and Overview ............................................................... 12 IIB Conservation Measures ................................................................................................. 18 IIC Analytical Framework for the Jeopardy and Adverse Modification Determination ..... 22 III PALLID STURGEON....................................................................................................... 24 IIIA Pallid Sturgeon - Status of the Species/Critical Habitat ................................................ 24 IIIB Pallid Sturgeon - Environmental Baseline..................................................................... 34 IIIC Pallid Sturgeon - Effects of the Action .......................................................................... 46 IIID Pallid Sturgeon - Cumulative Effects ............................................................................ 59 IIIE Pallid Sturgeon - Conclusion ......................................................................................... 60 IV INTERIOR LEAST TERN ................................................................................................ 62 IVA Interior Least Tern - Status of the Species/Critical Habitat ........................................... 62 IVB Interior Least Tern - Environmental Baseline ............................................................... 78 IVC Interior Least Tern - Effects of the Action .................................................................... 80 IVD Interior Least Tern - Cumulative Effects ..................................................................... 101 IVE Interior Least Tern - Conclusion ................................................................................. 102 V PIPING PLOVER ................................................................................................................ 105 VA Piping Plover – Status of the Species/Critical Habitat ................................................ 105 VB Piping Plover - Environmental Baseline ..................................................................... 117 VC Piping Plover - Effects of the Action and Species Response ...................................... 119 VD Piping Plover - Cumulative Effects ............................................................................. 131 VE Piping Plover - Conclusion .......................................................................................... 132 VI Incidental Take Statement ............................................................................................... 135 VIA Amount and Extent of Take (Pallid Sturgeon) ............................................................ 135 VIB Amount or Extent of Take (Interior Least Tern) ......................................................... 137 VIC Amount or Extent of Take (Piping Plover) ................................................................. 139 VII CONSERVATION RECOMMENDATIONS ................................................................ 141 VIII REINITIATION NOTICE ............................................................................................... 142 Biological Opinion – Project No. 1256-031 i APPENDIX A—Request for Consultation APPENDIX B—Service Approach to Evaluating Effects of the Proposed Action in the Biological Opinion APPENDIX C— Species List APPENDIX D—Hydrology and River Geomorphology under Environmental Baseline and Staff Alternative .......................................................................................................................... APPENDIX E—Extended Discussion of Project Hydrocycling APPENDIX F—Supplemental Scientific and Commercial Information Considered in the Opinion APPENDIX G—Literature Cited Biological Opinion – Project No. 1256-031 ii TABLE OF FIGURES Figure 1. Action area depicting Loup River Bypassed Reach, Platte River Bypassed Reach, and Lower Platte River (Source: USFWS). ........................................................................... 9 Figure 2. Expanded Loup River Bypassed Reach with important stream and gage locations (Source: USFWS). ............................................................................................................... 10 Figure 3. Expanded Lower Platte River with important river and gage locations (Source: USFWS). ............................................................................................................................. 11 Figure 4. Project Footprint (Source: USFWS). ................................................................................... 12 Figure 5. Portion of Project from the diversion to the Monroe Powerhouse (Source: USFWS). ............................................................................................................................. 13 Figure 6. Portion of the Project between Monroe Powerhouse and Lake Babcock (Source: USFWS). ............................................................................................................................. 15 Figure 7. Portion of the Project from Lake Babcock to Platte River (Source: USFWS). ................... 16 Figure 8. Current Range of the Pallid Sturgeon (Source: USFWS 2014a) ........................................ 26 Figure 9. Central Lowlands Management Unit (Source: USFWS 2014a) ......................................... 28 Figure 10. Streamflow variables for the Platte River at North Bend. Red box identifies the time period when run-of-canal operations are to be maintained (Source: USFWS). .......... 48 Figure 11. Flow-related conservation measures proposed by the Commission for the Loup River Bypassed Reach and the Lower Platte River (Source: USFWS). Also displayed is the spring, summer, and fall time periods described in Hamel et al. (2014a). ................................................................................................................................ 49 Figure 12. Hydrograph of the Ashland stream gage located near the pallid sturgeon fish kill that occurred on July 19, 2012 (Source: USGS). ................................................................. 53 Figure 13. Current range of Interior and coastal populations of the least tern including the 4 major geographical breeding populations of the Interior least tern. Numbers represent discrete breeding subpopulations, based upon dispersal distances. Reproduced from Service Interior least tern 5-year review, 2014, originally in Lott (2012). ................................................................................................................................. 63 Figure 14. Annual Interior least tern counts and trend line, 1986 - 2012, Upper Missouri River, South (Pavelka in litt. 2012). Reproduced from Service Interior least tern 5- year review. ......................................................................................................................... 68 Figure 15. Interior least tern annual adult counts and runoff in the Missouri River above Sioux City, Iowa, 1986 - 2012 (Pavelka in litt. 2012). Reproduced from Service Interior least tern 5-year review. ....................................................................................................... 68 Figure 16. Interior least tern counts on the Niobrara River, 2000 - 2012 (compiled from Yager in litt. 2012b, Hicks et al. 2012, Jenninges in litt. 2012, Lott 2006). Reproduced from Service Interior least tern 5-year review. .................................................................... 69 Figure 17. Interior least tern counts on the Loup River, 1985-2015 (NGPC data from: FLA Appendix E-2 USFWS Nebraska Field Office data 2010-2012, 2014c). ............................ 70 Figure 18. Number of Interior least tern nests on sandbars v. sand mine spoil on the lower Platte River, 2006 – 2011 (Jorgensen and Brown 2012). .................................................... 71 Biological Opinion – Project No. 1256-031 iii Figure 19. Range of piping plover. Source: Reproduced from USFWS 2009b Piping Plover 5- year Review. ...................................................................................................................... 111 Figure 20. Areas of the Loup River surveyed in 2010 and 2012. (Modified from Figure 1, USFWS (2010)). The Lower Platte River has been surveyed annually since 2008. ........ 115 Biological Opinion – Project No. 1256-031 iv TABLE OF TABLES Table 1. Species considered in the Commission’s 2014 analyses for the Staff Alternative and effect determinations. ...................................................................................................... 7 Table 2 Annual total number of pallid sturgeon captures in the Lower Platte River (Source Hamel 2014a as modified by USFWS). .............................................................................. 36 Table 3. Pallid