Methow River Subbasin Effectiveness Monitoring Program – Final Report U.S. Department of the Interior Bureau of Reclamation Pacific Northwest Region Boise, ID August 2019 Mission Statements The mission of the Department of the Interior is to protect and manage the Nation’s natural resources and cultural heritage; provide scientific and other information about those resources; and honor its trust responsibilities or special commitments to American Indians, Alaska Natives, and affiliated island communities. 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. Methow River Subbasin Effectiveness Monitoring Program – Final Report Prepared for Pacific Northwest Region, Bureau of Reclamation Prepared by Inter-Fluve, Inc. Mackenzie Baxter Joe Parzych Gardner Johnston BioAnalysts, Inc. Tracy Hillman, Ph.D. Methow River Subbasin Effectiveness Monitoring Program Report Contents Page 1 Executive Summary ...............................................................................................4 1.1 Habitat Enhancement Actions ............................................................................4 1.2 Status and Trends Monitoring ............................................................................6 1.3 Action Effectiveness Monitoring .......................................................................6 1.4 Ecological Models .............................................................................................7 1.5 Integrating Lessons Learned ..............................................................................9 2 Introduction ..........................................................................................................10 2.1 Overview ..........................................................................................................10 2.2 Action Agency Tributary Habitat Improvement Efforts ..................................12 2.3 Summary of Methow Effectiveness Monitoring Program ...............................13 2.4 Methow Effectiveness Monitoring Effort Coordination and History ..............15 3 Habitat Enhancement in the Methow ................................................................17 3.1 Habitat Enhancement Programs and Cooperating Entities ..............................17 3.2 Action Types and Locations ............................................................................19 3.2.1 Instream Flow Improvement ......................................................................20 3.2.2 Fish Screening ............................................................................................21 3.2.3 Fish Passage and Access ............................................................................22 3.2.4 Stream and Floodplain Enhancement ........................................................23 3.2.5 Riparian Rehabilitation ..............................................................................24 3.2.6 Acquisitions and Easements ......................................................................25 3.3 Subbasin Implementation Context ...................................................................27 4 Status and Trends Monitoring ............................................................................31 4.1 Spawner Abundance ........................................................................................31 4.2 Juvenile Production and Survival ....................................................................35 4.3 Life Cycle Monitoring .....................................................................................41 5 Habitat Action Effectiveness Monitoring ..........................................................44 5.1 M2 Reach BACI Study ....................................................................................44 5.1.1 Overview and Methods ..............................................................................44 5.1.2 Fish and Habitat Relationships (pre-treatment) .........................................48 5.1.3 Fish Population Response (post-treatment) ...............................................50 5.2 Food Web Study ..............................................................................................56 5.2.1 Overview and Methods ..............................................................................56 5.2.2 Study Findings ...........................................................................................56 5.3 Beaver Creek ....................................................................................................58 5.3.1 Overview ....................................................................................................58 5.3.2 Study Findings ...........................................................................................61 5.4 Other Studies ....................................................................................................64 5.4.1 Elbow Coulee .............................................................................................64 5.4.2 Hancock Springs ........................................................................................64 5.4.3 Groundwater-Surface Water Exchange .....................................................65 5.4.4 Stream Metabolism Variability ..................................................................65 5.4.5 Entiat River ................................................................................................66 6 Aquatic Trophic Productivity Model .................................................................67 6.1 Model Background...........................................................................................67 i Methow River Subbasin Effectiveness Monitoring Program Report 6.2 Model Parameters ............................................................................................68 6.3 Model Parameterization and Validation ..........................................................69 6.4 Model Results ..................................................................................................69 6.5 Model Interpretation ........................................................................................71 7 Key Findings and Lessons Learned ...................................................................72 7.1 Fish Use Patterns, Trends, and Responses to Enhancement Actions ..............72 7.2 Fish Passage Improvements .............................................................................75 7.3 Floodplain and Side Channel Habitat Enhancement .......................................76 7.4 Enhancement of Channel Complexity .............................................................79 7.5 Food Web Dynamics........................................................................................81 7.6 Recommendations ............................................................................................82 8 References .............................................................................................................84 Appendices Appendix A – Enhancement Action List Appendix B – Annotated Bibliography ii Methow River Subbasin Effectiveness Monitoring Program Report Acknowledgments Numerous individuals were involved with the preparation and review of this report and we thank them for their assistance. This was a collaborative effort with Reclamation and we very much appreciate the regular review and input by Mitch Mumma, Jude Trapani, Jennifer Molesworth, Vince Kozakiewicz, and early on by Kate Puckett. Grace Watson, with the Methow Salmon Recovery Foundation, was a regular part of the project team and provided valuable assistance and technical input. We very much thank the five peer reviewers who reviewed the early draft and provided technical and editorial input that significantly improved the final report. These include Casey Baldwin with Colville Confederated Tribes, Carlos Polivka with the US Forest Service, George Pess with NOAA Fisheries, Brandon Rogers with the Yakama Nation, and Charlie Snow with Washington Department of Fish and Wildlife. We also thank Joe Benjamin (USGS) and Ryan Bellmore (USFS) for their information and assistance with the ATP Model. Other individuals also provided input, including members of the Methow Restoration Council, and we thank them for their review and contributions. iii Methow River Subbasin Effectiveness Monitoring Program Report 1 Executive Summary In this report, the Pacific Northwest Region of the Bureau of Reclamation (Reclamation) summarizes research, monitoring, and evaluation (RM&E) activities associated with tributary habitat improvements that support salmon and steelhead in the Methow Basin that are listed under the Endangered Species Act (ESA). The Methow River is a tributary of the Columbia River. Since the listings, Reclamation invested significant resources in both RME and tributary habitat improvement activities in the Methow Basin as one aspect of implementing the Federal Columbia River Power System (FCRPS) Biological Opinion (BiOp). In this BiOp, Reclamation, with the Corps of Engineers (COE) and Bonneville Power Administration (BPA) consulted with NOAA Fisheries, on the continued operation and maintenance of the FCRPS. Reclamation operates Grand Coulee and Hungry Horse dams, 2 of the 14 dams covered in the FCRPS consultation. There are no FCRPS facilities in the Methow River or tributaries to the Methow River. Reclamation contributions