INSTREAM FLOWS RESEARCH AND VALIDATION METHODOLOGY FRAMEWORK 2016–2017 Guadalupe, San Antonio, Mission, and Aransas Rivers and Mission, Copano, Aransas, and San Antonio Bays Basin FINAL REPORT Prepared for Texas Water Development Board Prepared by San Antonio River Authority Dr. Timothy Bonner (Texas State University) Dr. Jacquelyn Duke (Baylor University) BIO-WEST, Inc. August 15, 2017 PURSUANT TO HOUSE BILL 1 AS APPROVED BY THE 84TH TEXAS LEGISLATURE, THIS STUDY REPORT WAS FUNDED FOR THE PURPOSE OF STUDYING ENVIRONMENTAL FLOW NEEDS FOR TEXAS RIVERS AND ESTUARIES AS PART OF THE ADAPTIVE MANAGEMENT PHASE OF THE SENATE BILL 3 PROCESS FOR ENVIRONMENTAL FLOWS ESTABLISHED BY THE 80TH TEXAS LEGISLATURE. THE VIEWS AND CONCLUSIONS EXPRESSED HEREIN ARE THOSE OF THE AUTHOR(S) AND DO NOT NECESSARILY REFLECT THE VIEWS OF THE TEXAS WATER DEVELOPMENT BOARD. Table of Contents Table of Contents 1 Introduction .............................................................................................................................. 1 1.1 Aquatic ........................................................................................................................... 3 1.1.1 Study Objectives ....................................................................................................................... 4 1.2 Riparian .......................................................................................................................... 4 1.2.1 Study Questions and Hypotheses ............................................................................................. 7 1.3 Floodplains ..................................................................................................................... 8 1.3.1 Study Objectives ....................................................................................................................... 9 2 Methods and Materials ............................................................................................................ 9 2.1 Aquatics ......................................................................................................................... 9 2.1.1 Aquatic Field Studies ............................................................................................................. 10 2.1.2 Aquatic Historical Analysis .................................................................................................... 13 2.2 Riparian ........................................................................................................................ 14 2.2.1 Field Sampling ....................................................................................................................... 15 2.2.2 Estimate of Inundation ........................................................................................................... 17 2.2.3 Statistical Analyses ................................................................................................................. 18 2.3 Floodplains ................................................................................................................... 19 3 Results, Discussion, and Interdisciplinary Assessment ......................................................... 22 3.1 Aquatics ....................................................................................................................... 22 3.1.1 Aquatic Field Studies ............................................................................................................. 22 3.1.2 Aquatic Historical Analysis .................................................................................................... 50 3.2 Riparian ........................................................................................................................ 54 3.2.1 Goliad Site .............................................................................................................................. 54 3.2.2 Gonzales Site .......................................................................................................................... 58 3.2.3 Community and Basin Assessments ....................................................................................... 66 3.2.4 Comparison of Methodologies ............................................................................................... 66 3.2.5 Conclusions ............................................................................................................................ 68 3.3 Floodplain .................................................................................................................... 69 3.3.1 Fish Communities ................................................................................................................... 69 3.3.2 Connection Discharges ........................................................................................................... 71 3.3.3 Standards Evaluation .............................................................................................................. 72 4 Multidisciplinary Evaluation ................................................................................................. 73 4.1 Summary of Key Ecological Components ................................................................... 73 4.1.1 Aquatics .................................................................................................................................. 73 4.1.2 Riparian .................................................................................................................................. 73 4.1.3 Floodplains ............................................................................................................................. 74 Instream Flows Research and Validation Methodology Framework August 2017 TWDB 2016–2017 i TWDB Contract # 1600011937 Table of Contents 4.1.4 Ecological Response Summary .............................................................................................. 74 4.1.5 Validation Methodology Assessment Tool ............................................................................ 75 5 Recommendations for Future Applied Research and Long-Term Monitoring ..................... 75 5.1 Focused Applied Research ........................................................................................... 75 5.2 Long-term Monitoring ................................................................................................. 76 6 Acknowledgements ................................................................................................................ 76 7 References .............................................................................................................................. 76 List of Figures Figure 1. Reference map of locations within the GSA (taken from GSA BBEST 2011). Specific sites used in this study are reported in the text. ......................................... 10 Figure 2. An example site showing 75 random points selected within each level. (Image source: Google Earth.) ............................................................................................. 16 Figure 3. Example GIS screenshot showing water’s edge, quadrats, mature trees, and elevation contours. ................................................................................................... 18 Figure 4. Lower Guadalupe River floodplain lakes evaluated as part of this study. ............... 20 Figure 5. Hydrograph from USGS gage # 08173900 on the Guadalupe River—Gonzales from 2011 to 2017 showing Round One (dashed line) and Round Two (dotted line) sampling periods. ..................................................................................................... 23 Figure 6. Relative abundances among tier and flow magnitudes for slack-water fishes (top), moderately swift-water fishes (middle), and swift-water fishes (bottom) in riffle habitats. .................................................................................................................... 26 Figure 7. Relative abundances among flow tiers at Guadalupe River—Comfort and Medina River—Bandera in riffle habitats. Black circles represent pre-flood estimates; open circles represent post-flood estimates. ..................................................................... 27 Figure 8. Densities (number of individuals per m2) among flow tiers at Guadalupe River— Comfort and Medina River—Bandera in riffle habitats. Black circles represent pre- flood estimates; open circles represent post-flood estimates. .................................. 28 Figure 9. Relative abundances among flow tiers at Guadalupe River—Gonzales, Guadalupe River—Cuero, and San Antonio—Goliad in riffle habitats. Black circles represent pre-flood estimates; open circles represent post-flood estimates. ........................... 30 Figure 10. Densities among flow tiers at Guadalupe River—Gonzales, Guadalupe River— Cuero, and San Antonio—Goliad in riffle habitats. Black circles represent pre-flood estimates; open circles represent post-flood estimates. ........................................... 31 Instream Flows Research and Validation Methodology Framework August 2017 TWDB 2016–2017 ii TWDB Contract # 1600011937 Table of Contents Figure 11. Relative abundances among flow tiers at Cibolo Creek—Falls City in riffle habitats. Black circles represent pre-flood estimates; open circles represent post-flood estimates. .................................................................................................................. 32 Figure 12. Density among