Developing Environmental Flows for Fish and Wildlife: A Mesohabitat Study on the Niobrara River Revised Final Report June 2014 Developing Environmental Flows for Fish and Wildlife: A Mesohabitat Study on the Niobrara River by Rushing Rivers Institute and University of Lincoln, Nebraska Authors: Piotr Parasiewicz, Mark Pegg, Joseph Rogers, Adam Behmer, Allan Eldridge for Nebraska Game and Parks Commission June 2014 Acknowledgements This project was funded by the Nebraska Game and Parks Commission through the Sportfish Restoration Act. We would like to acknowledge the following organizations for their assistance in compiling data and for their input throughout the development of this report: Nebraska Game and Parks Commission (Richard Holland and Larry Hutchison for project guidance and assistance, Michelle Koch and Rachel Simpson for access to Nebraska Heritage data); US Fish and Wildlife Service (Ft. Niobrara staff; Greg Wanner – fish data); National Park Service (Pam Sprenkle - assistance in access, permitting, and logistic concerns); Nebraska Department of Environmental Quality (Ken Bazata - REMAP); Nebraska State Highway Patrol (Lt. Frank Peck - aerial reconnaissance); US Geological Survey (Jason Alexander - GIS data and geomorphic delineation); and Drs. Edward Peters and James Parham for supporting information from the Platte River habitat suitability assessment. Table of Contents Acknowledgements ......................................................................................................................... iii List of Figures .................................................................................................................................. vi List of Tables ................................................................................................................................. viii List of Appendices ............................................................................................................................ x Glossary ........................................................................................................................................... xi Executive Summary ......................................................................................................................... 1 Chapter 1.0: Project Introduction ................................................................................................. 10 Purpose, Objectives and Content ............................................................................................. 10 Scope of Work ........................................................................................................................... 10 Goals ......................................................................................................................................... 11 Objectives and Tasks ................................................................................................................. 11 MesoHABSIM ............................................................................................................................ 11 Data Sources ............................................................................................................................. 14 Reports .................................................................................................................................. 14 Notable Resources ................................................................................................................ 14 GIS Data ................................................................................................................................. 15 Chapter 1.1: Watershed Description ............................................................................................ 15 Geographical Settings of the Niobrara River ............................................................................ 15 Human History of the Watershed ......................................................................................... 16 Status Quo of Water Uses ..................................................................................................... 16 Chapter 1.2: Project Setup ............................................................................................................ 18 Spatial Scale Terminology ......................................................................................................... 18 Study Area and Section Delineation ..................................................................................... 19 Selection of Representative Sites ......................................................................................... 20 CFS and CFSM ........................................................................................................................ 23 Habitat Mapping Surveys ...................................................................................................... 25 Avifauna Habitat Surveys ...................................................................................................... 27 Study Sections ....................................................................................................................... 27 Chapter 1.3: Hydrology ................................................................................................................. 33 Hydrology and Time Series Development ................................................................................ 33 Introduction .......................................................................................................................... 34 Methods ................................................................................................................................ 34 Data Processing ..................................................................................................................... 34 Data Development ................................................................................................................ 35 Chapter 1.4: Freshwater Ecology .................................................................................................. 35 Bioperiods and Flow Needs ...................................................................................................... 35 Targeted Species and Communities ......................................................................................... 36 Fish Community .................................................................................................................... 37 Fish Species of Special Interest ................................................................................................. 39 Avifauna .................................................................................................................................... 39 Chapter 1.5: Fish and Bird Habitat ................................................................................................ 41 Existing Fish Community (XFC) and Habitat Associations ..................................................... 41 Suitability Models ..................................................................................................................... 49 Introduction .......................................................................................................................... 49 Methods ................................................................................................................................ 49 Final Species Modeling Plan .................................................................................................. 52 Habitat Rating Curves ........................................................................................................... 56 Fish and Bird Habitat Rating Curve Results by Segment .......................................................... 53 Chapter 1.6: Habitat Time Series Analysis .................................................................................... 61 Introduction .............................................................................................................................. 61 Results ....................................................................................................................................... 64 Flow Guideline Criteria ............................................................................................................. 66 Discussion ................................................................................................................................. 68 Chapter 1.7: Flow Guideline Scheme ............................................................................................ 75 REFERENCES .................................................................................................................................. 77 List of Figures Figure 1: Study area for the Niobrara River. Map shows section and site locations. .................... 2 Figure 2: Community rating curves for Segment 1 (Sites 1-3) in the Niobrara River. .................... 5 Figure 3: A comparison of the expected fish community (XFC) for Segment 1 with the model results at three flow levels. ............................................................................................................. 5 Figure 4: ACTogram for the Rearing & Growth bioperiod relevant to the Verdel Gage. ............... 8 Figure 5: ACTogram for the Rearing & Growth bioperiod relevant to the Sparks Gage. ............... 8 Figure 6: A simplified schematic illustrating the key