Technical Assessments in Support of the Edwards Aquifer Science Committee “J Charge” Flow Regime Evaluation for the Comal and San Marcos River Systems Prepared for: The Edwards Aquifer Recovery and Implementation Program Prepared by: Dr. Thomas B. Hardy, Ph.D. River Systems Institute Texas State University San Marcos, Texas December 29, 2009 Acknowledgments Many individuals from private, local, state, and federal agencies contributed to the development of material summarized in this report. Without their input and efforts, this report would not have been possible. Although the list of individual who in some manner contributed to the data, modeling results, or scientific material used in this report is extensive and too long to list, the following individuals are acknowledged as having made significant contributions in terms of both their time and expertise. The author apologizes for inclusion of anyone who does not wish to be acknowledged or to anyone whom I have failed to properly acknowledge. Dr. Mara Alexander Mr. William Amy Mr. Karim Aziz Ms. Megan Bean Dr. Timothy Bonner Dr. Tom Brandt Ms. Jean Cochrane Mr. Pat Conner Ms. Melani Howard Mr. Praveen Kokkanti Mr. Brad Littrell Mr. Miguel Mora Mr. Ed Orborny Mr. Nathan Pence Ms. Jackie Poole Mr. Kenny Saunders Ms. Jenna Winters Mr. Adam Zerringer Table of Contents Acknowledgments ..................................................................................................................................... ii Executive Summary ................................................................................................................................... x Introduction ................................................................................................................................................ 1 Study Areas ................................................................................................................................................ 1 Comal .................................................................................................................................................... 1 San Marcos ............................................................................................................................................ 3 Influence Diagrams for Target Species ...................................................................................................... 4 Comal Springs Riffle Beetle .................................................................................................................. 5 Texas Wild Rice ..................................................................................................................................... 9 Fountain Darters .................................................................................................................................. 10 Hydrodynamic Modeling ......................................................................................................................... 13 Physical Characterization .................................................................................................................... 13 Development of Computational Meshes ............................................................................................. 14 Two-dimensional Hydraulic Models ................................................................................................... 15 Water Surface Elevation Modeling ................................................................................................. 16 Comal River .................................................................................................................................... 17 San Marcos River ........................................................................................................................... 20 San Marcos No Cape's Dam Alternative Modeling Scenario .................................................... 22 Vegetation Mapping ............................................................................................................................ 22 Vegetation Dependent Hydraulic Roughness ...................................................................................... 23 Vertical Velocity Distributions in Vegetation ...................................................................................... 25 Water Quality and Temperature Modeling ............................................................................................... 25 Comal River ........................................................................................................................................ 25 Boundary Conditions ...................................................................................................................... 28 Model Calibration and Verification ................................................................................................ 30 San Marcos River ................................................................................................................................ 31 Boundary Conditions ...................................................................................................................... 31 Model Calibration and Verification ................................................................................................ 34 Habitat Suitability Curves ........................................................................................................................ 35 Comal Springs Riffle Beetle ................................................................................................................ 36 Texas Wild Rice ................................................................................................................................... 37 Fountain Darters .................................................................................................................................. 40 Physical Habitat Modeling ....................................................................................................................... 44 Comal Springs Riffle Beetle Habitat Equation ................................................................................... 45 Texas Wild Rice Habitat Equation ...................................................................................................... 45 Fountain Darter Habitat Equation ....................................................................................................... 45 Modeling Results and Discussion ............................................................................................................ 45 Comal .................................................................................................................................................. 46 Temperature .................................................................................................................................... 46 Dissolved Oxygen........................................................................................................................... 48 Comal Springs Riffle Beetle ........................................................................................................... 50 Fountain Darter ............................................................................................................................... 52 System-Wide Physical Habitat Using Mean Daily Temperatures ............................................. 52 Physical Habitat Using Maximum Daily Temperatures ............................................................ 54 San Marcos .......................................................................................................................................... 60 Temperature .................................................................................................................................... 60 Dissolved Oxygen........................................................................................................................... 62 Texas Wild Rice .............................................................................................................................. 62 System-Wide Physical Habitat ................................................................................................... 62 Spring Lake ................................................................................................................................ 63 Rio Vista ..................................................................................................................................... 63 Above Cape’s ............................................................................................................................. 64 Mill Race .................................................................................................................................... 64 State Hatchery A ........................................................................................................................ 64 State Hatchery B ........................................................................................................................ 64 Lower San Marcos A ................................................................................................................. 64 Lower San Marcos B ................................................................................................................. 65 Revised Upper San Marcos Physical Habitat Modeling ................................................................ 65 Texas