Management Plan for Endangered Fishes in the Yampa River Basin Environmental Assessment Gerald W. Roehm U.S. Fish and Wildlife Service Denver, Colorado September 2004 Recommended citation: Roehm, G. W. 2004. Management plan for endangered fishes in the Yampa River Basin and environmental assessment. U.S. Fish and Wildlife Service, Mountain-Prairie Region (6). Denver. Management Plan for Endangered Fishes in the Yampa River Basin ii MANAGEMENT PLAN FOR ENDANGERED FISHES IN THE YAMPA RIVER BASIN AND ENVIRONMENTAL ASSESSMENT Prepared by Gerald W. Roehm Instream Flow Coordinator U.S. Fish and Wildlife Service Upper Colorado River Endangered Fish Recovery Program P.O. Box 25486, DFC Denver, Colorado 80225-0486 Final Upper Colorado River Endangered Fish Recovery Program Project No. C-9 September 2004 Management Plan for Endangered Fishes in the Yampa River Basin iii ACKNOWLEDGMENTS This management plan was funded by the Recovery Implementation Program for Endangered Fish Species in the Upper Colorado River Basin. The Recovery Program is a joint effort of the U.S. Fish and Wildlife Service, U.S. Bureau of Reclamation, Western Area Power Administration, states of Colorado, Utah, and Wyoming, Upper Basin water users, environmental organizations, the Colorado River Energy Distributors Association, and the National Park Service. The author wishes to thank Ray Alvarado, Bob Muth, Tom Nesler, John Shields, George Smith; Ray Tenney and Robert Wigington for their significant contributions to the content of this management plan. In addition, the author would like to acknowledge Margot Zallen for her extensive legal and editorial review; Patty SchraderGelatt for her valuable input to and review of the management plan; and Kathy Wall, Debbie Felker, Amie Hart and Ellen Szczesny, Recovery Program staff, for their administrative, editorial, and technical assistance. Thanks also go to the Yampa River Basin Partnership which provided a forum for local public participation in project planning and development; Ayres Associates and Pioneer Environmental Services for technical assistance; and members of the Yampa Project Management Team and Yampa Programmatic Biological Opinion Workgroup, who provided their advice and technical expertise: Ray Alvarado, Dan Birch, Greg Espegren, Paul Flack, Bill Haffner, Don Halffield, John Hamill, Tom Iseman, Eric Kuhn, Henry Maddux, Dave Mazour, Dan McAuliffe, Bob Muth, Brian Nazarenus, Tom Nesler, Tom Pitts, Bob Plaska, John Shields, George Smith, Ray Tenney, Brent Uilenberg, and Robert Wigington. Management Plan for Endangered Fishes in the Yampa River Basin iv TABLE OF CONTENTS LIST OF TABLES .........................................................x LIST OF FIGURES ...................................................... xiii ACRONYMS, ABBREVIATIONS AND UNITS OF MEASURE ...........xv EXECUTIVE SUMMARY .............................................. xvii MANAGEMENT PLAN INTRODUCTION ............................................................1 Purpose and Need .........................................................1 Setting ...................................................................3 Status and Current Distribution of Endangered Fish Species .....................9 Humpback chub (Gila cypha) ............................................12 Bonytail (Gila elegans) ..................................................14 Colorado pikeminnow (Ptychocheilus lucius) ...............................15 Razorback sucker (Xyrauchen texanus) ....................................16 DESCRIPTION OF THE PROPOSED ACTION .................................18 Historic, Current and Projected Depletions ...................................18 Colorado Depletions ...................................................18 Wyoming Depletions ...................................................25 Water Rights Administration ...............................................29 Depletion Accounting .....................................................30 Framework for Recovery Actions and Cooperative Agreement ...................31 Provide and Protect Instream Flows .........................................32 Background ..........................................................32 Quantification of Augmentation Needs ....................................36 Formulation of an Augmentation Strategy .................................42 Description of Alternatives ..............................................44 Non-structural alternatives .............................................44 Structural alternatives ................................................46 Other alternatives considered ...........................................47 Management Plan for Endangered Fishes in the Yampa River Basin v TABLE OF CONTENTS (continued) Evaluation of Alternatives ...............................................51 Ability to meet base-flow needs ........................................51 Comparison of estimated costs .........................................54 Impacts to parks and water-related recreation ..............................56 Impacts on agriculture ................................................66 Impacts on peak flows ................................................68 Legal and institutional constraints .......................................71 Evaluation summary .................................................73 Proposed action for Base-flow Augmentation ...............................75 Reduce Negative Impacts of Nonnative Fishes .................................79 Background ..........................................................79 Nonnative Fish Management Policy .......................................81 Nonnative Stocking Procedures ..........................................81 Aquatic Wildlife Management Plan .......................................82 Upper Yampa River ..................................................82 Middle Yampa River .................................................82 Lower Little Snake River ..............................................83 Lower Yampa River ..................................................83 Green River within Colorado ...........................................83 Elkhead Reservoir — Lake Management Plan ..............................83 Proposed Control Actions for Nonnative Fishes in the Yampa River ...........85 Implementation of Nonnative Stocking Procedures .........................85 Non-lethal removal and translocation of northern pike and smallmouth bass .....86 Lethal removal of channel catfish and smallmouth bass from Yampa Canyon ....92 Removal of angler bag and possession limits in Colorado ....................93 Containing escapement from Elkhead Reservoir ............................93 Information and education .............................................98 Restore Habitat (Habitat Development and Maintenance) .......................99 Acquire and enhance floodplain habitats ..................................99 Restore/maintain native fish passage at diversion structures .................101 Evaluate/remediate entrainment by diversion structures ....................102 Management Plan for Endangered Fishes in the Yampa River Basin vi TABLE OF CONTENTS (continued) Manage Genetic Diversity/Augment or Restore Populations ....................102 Monitor Populations and Habitat ..........................................103 Monitoring endangered fish populations ..................................104 Monitoring nonnative/native fish populations .............................105 Monitoring habitat ....................................................105 Monitoring flow....................................................105 Monitoring sediment transport.........................................106 Other monitoring...................................................107 ENVIRONMENTAL ASSESSMENT INTRODUCTION ..........................................................108 PURPOSE AND NEED ......................................................109 AFFECTED ENVIRONMENT ...............................................110 Geography and topography ...............................................110 Climate ................................................................110 Geology and soils ........................................................110 Hydrology and geomorphology ............................................111 Water quality ...........................................................112 Air quality ..............................................................126 Vegetation ..............................................................127 Wildlife ................................................................134 Fisheries ...............................................................141 Threatened and endangered species ........................................144 Bald eagle ...........................................................144 Mexican spotted owl ..................................................145 Southwestern willow flycatcher .........................................145 Humpback chub ......................................................145 Bonytail .............................................................145 Colorado pikeminnow .................................................146 Razorback sucker .....................................................146 Management Plan for Endangered Fishes in the Yampa River Basin vii TABLE OF CONTENTS (continued) Black-footed ferret ....................................................146 Canada lynx .........................................................146