Edwards Aquifer Recovery Implementation Program Habitat Conservation Plan November 2012 Prepared For Dr. Robert L. Gulley Program Manager Edwards Aquifer Recovery Implementation Program Prepared By RECON Environmental, Inc. Hicks & Company Zara Environmental LLC BIO-WEST Edwards Aquifer Recovery Implementation Program HABITAT CONSERVATION PLAN TABLE OF CONTENTS Chapter 1 Introduction 1-1 1.1 Background 1-1 1.2 Permit Area 1-7 1.3 Permit Holders and Permit Duration 1-7 1.4 Species Proposed for Coverage under the Permit 1-9 1.5 Regulatory Framework 1-11 1.6 Alternatives Considered during the Development of the HCP 1-15 1.7 Public Involvement 1-18 Chapter 2 Activities Covered by the Permit 2-1 2.1 Covered Activities 2-1 2.2 Edwards Aquifer Authority 2-1 2.3 City of New Braunfels 2-7 2.4 City of San Marcos 2-10 2.5 Texas State University 2-12 2.6 San Antonio Water System 2-16 2.7 Texas Parks and Wildlife Department 2-16 2.8 Adaptive Management Process 2-16 Chapter 3 Environmental Setting and Baseline Conditions 3-1 3.1 Climate 3-1 3.2 Aquifer-fed Springs 3-24 3.3 Edwards (Balcones Fault Zone) Aquifer 3-31 3.4 The Edwards Aquifer, Comal Springs, and San Marcos Springs 3-45 3.5 Listed Species Covered by the ESA Section 10(a)(1)(b) Incidental Take Permit 3-55 3.6 Species Warranted for Listing Covered by the Section 10(a)(1)(B) Permit, If listed in the future 3-67 Chapter 4 Covered Species Analysis 4-1 4.0 Introduction 4-1 4.1 Long Term Biological Goals and Objectives 4-2 4.2 Potential Impacts to and Incidental Take of Covered Species 4-36 Chapter 5 Minimization and Mitigation Measures; Measures Specifically Intended to Contribute to Recovery 5-1 ii Edwards Aquifer Recovery Implementation Program HABITAT CONSERVATION PLAN 5.0 Approach to the Implementation of the Minimization and Mitigation Measures 5-1 5.1 Edwards Aquifer Authority 5-3 5.2 City of New Braunfels 5-10 5.3 City of San Marcos 5-20 5.4 Texas State University 5-29 5.5 San Antonio Water System 5-37 5.6 Texas Parks and Wildlife Department 5-40 5.7 Measures that Specifically Contribute to Recovery 5-41 5.8 HDR’s Analysis of the Springflow Protection Measures 5-44 5.9 EAA’s Authority to Implement Measures to Maintain Springflow Prior to the Complete Implementation of the Phase I Package 5-56 Chapter 6 Adaptive Management Program 6-1 6.1 Adaptive Management Process 6-1 6.2 Monitoring 6-1 6.3 Adaptive Management Research and Modeling for the Phase I Adjustments and Phase II Strategic Adaptive Management Decisions 6-3 6.4 Core Adaptive Management Actions 6-14 Chapter 7 Costs and Funding 7-1 7.0 Introduction 7-1 7.1 Phase I Measures 7-1 7.2 Funding Assurances for Any Additional Phase II Measures 7-6 7.3 Alternative Funding 7-7 Chapter 8 Changed Circumstances, Unforeseen Circumstances, No Surprises, and Other Federal Commitments 8-1 8.0 Introduction 8-1 8.1 Changed Circumstances 8-1 8.2 Unforeseen Circumstances 8-7 8.3 Additional Federal Commitments 8-10 Chapter 9 Permit Administration 9-1 9.1 Governance 9-1 9.2 Permit Amendments 9-3 9.3 Annual Reporting 9-4 9.4 Subsequent Listing of Covered Species 9-5 iii Edwards Aquifer Recovery Implementation Program HABITAT CONSERVATION PLAN Chapter 10 Preparers and Contributors 10-1 Chapter 11 Abbreviations and Acronyms 11-1 Chapter 12 Literature Cited 12-1 FIGURES 1-1: Edwards Aquifer 1-4 1-2: EARIP HCP Plan Area 1-8 1-3: Summary of Alternative Minimization and Mitigation Measures Considered 1-18 3-1: Climate Regions of Texas 3-2 3-2: Average Annual High Temperature (1971-2000) 3-3 3-3: Average Annual Precipitation (1971-2000) 3-4 3-4: Projected Precipitation Differences between 2009 and 2050 based on 3-9 3-5: Division 6 Rainfall 3-15 3-6: Division 6 Rainfall Frequency Distribution 3-17 3-7: Three-year Moving Average Rainfall 1895–2010 3-18 3-8: Five-year Moving Average Rainfall 1895–2010 3-18 3-9: Seven-year Moving Average Rainfall 1895–2010 3-19 3-10: Ten-year Moving Average Rainfall 1895–2010 3-19 3-11a: 1956 Photo of Landa Lake 3-22 3-11b: 1956 Photo of Landa Lake 3-23 3-12: General Location Map of Springs 3-25 iv Edwards Aquifer Recovery Implementation Program HABITAT CONSERVATION PLAN 3-13: Major Faults and Interpreted Groundwater Flowpaths to Comal and Hueco Springs 3-28 3-14: Cave Map of Fern Bank Springs 3-29 3-15: Geological Map showing the plotted Location of Fern Bank Springs Cave and Edwards Limestone Outcrop near the Blanco River 3-30 3-16 Various Segments of the Edwards Aquifer 3-33 3-17: Estimated Annual Recharge and 10 Year Floating Average of Charge For the San Antonio Segment (1934-2008) 3-43 3-18: Groundwater Pumping Compared to Springflow to the Edwards Aquifer 3-45 3-19a: Comal Springs Ecosystem Vicinity Map 3-48 3-19b: Comal Springs Ecosystem Vicinity Map 3-49 3-20a: San Marcos Springs Ecosystem Vicinity Map 3-51 3-20b: San Marcos Springs Ecosystem Vicinity Map 3-52 3-20c: San Marcos Springs Ecosystem Vicinity Map 3-42 3-53 4-1: Representative Sample Reaches—Comal Springs 4-3 4-2: Comal Springs Riffle Beetle Sample Area 4-11 4-3: Representative Sample Reaches—San Marcos Springs 4-25 4-4: San Marcos Salamander Sample Areas 4-32 4-5a: Direct Mortality Factors affecting the Fountain Darter and its Habitat 4-39 4-5b: Direct Mortality Factors affecting the Comal Springs Riffle Beetle and its Habitat 4-39 4-5c: Direct Mortality Factors affecting Texas Wild Rice 4-40 4-6a: Minimization and Mitigation Measures for Fountain Darter Impacts 4-43 v Edwards Aquifer Recovery Implementation Program HABITAT CONSERVATION PLAN 4-6b: Minimization and Mitigation Measures for Comal Springs Riffle Beetle Impacts 4-44 4-6c: Minimization and Mitigation Measures for Texas Wild-Rice 4-45 4-7: Appreciable Reduction in the Likelihood of Survival and Recovery 4-46 4-8: Modeled Comal Total Springflow for No Action Baseline, Existing Baseline, and HCP (Phase I) for 1947-2000 Model Period 4-50 4-9a: Modeled Comal Total Springflow for No Action Baseline, Existing Baseline, and HCP (Phase I and Phase II) for 1947-2000 Model Period 4-51 4-9b: Modeled HCP-Phase I Comal Total Discharge Relative to the Minimum Flow-Related Management Objective 4-54 4-9c: Modeled HCP-Phase II Comal Total Discharge Relative to the Minimum Flow-Related Management Objective 4-55 4-10a: Modeled San Marcos Total Springflow for No Action Baseline, Existing Baseline, and HCP (Phase I) for 1947-2000 Model Period 4-58 4-10b: Modeled San Marcos Total Springflow for the No Action Baseline, Existing Baseline, and HCP (Phase I and II) for the 1947-1957 Model Period. 4-59 4-10c: Modeled HCP-Phase I and Phase II San Marcos Total Discharge Relative to the Higher Flows Component of the Minimum Flow Objective 4-62 4-11: Stella Model Interface for Fountain Darter Habitat Model at Comal Springs 4-71 4-12: Habitat Quality Relationship for Bryophytes Versus Total Comal Springflow in the Upper Spring Run Reach 4-72 4-13: Total Comal Springflow Scenarios Evaluated in Stella 4-74 4-14: Total Fountain Darters within Representative Reaches – Comal System: (No Old Channel ERPA) 4-76 4-15: Total Fountain Darters within Representative Reaches – Comal System (with Old Channel ERPA) 4-77 vi Edwards Aquifer Recovery Implementation Program HABITAT CONSERVATION PLAN 4-16: Low Flow Representative Nine-Year Rolling Average (Total Comal Springflow) for HCP, No Action Baseline, and Existing Baseline modeled scenarios and historically observed(Old Channel ERPA) 4-79 4-17: Moderate Flow Representative Nine-Year Rolling Average (Total Comal Springflow) for the HCP, No Action Baseline, and Existing Baseline Modeled Scenarios and Historically Observed 4-80 4-18: High Flow Representative Nine-Year Rolling Average (Total Comal Springflow) for HCP, No Action Baseline, and Existing Baseline modeled scenarios and Historically observed 4-81 4-19: Modeled Fountain Darter Population at Comal Springs over the HCP Period for the HCP (with and without ERPA) and No Action Baseline 4-86 4-20: Modeled Fountain Darter Population at Comal Springs over the ITP for the HCP Phase I package and No Action Baseline 4-87 4-21: Modeled Wetted Area along Western Shoreline of Landa Lake and Spring Island at Total Daily Average Comal Discharge of 30 cfs 4-93 4-22: Stella Model Interface for Comal Springs Riffle Beetle Habitat Model at Comal Springs 4-96 4-23: Wetted Area to Flow Relationship for Spring Run 3 Sample Area 4-97 4-24: Total Comal Springflow current scenario (2002-2010) Evaluated in Stella 4-99 4-25: Comal Springs Riffle Beetles (within sample areas) Predicted by Stella Model 4-100 4-26: Total Comal Springs Riffle Beetles within Sample Areas Predicted during the Low-Flow Representative Period for the HCP-Phase I Package, No-Action Baseline, Existing Baseline, and the Historical Conditions—Comal System 4-103 4-27: Stella Model Interface for Fountain Darter Habitat Model at San Marcos Springs 4-119 4-28: Habitat Quality Relationship for Cabomba versus Total vii Edwards Aquifer Recovery Implementation Program HABITAT CONSERVATION PLAN San Marcos Springflow as a Daily Average in the City Park Reach 4-120 4-29: Total San Marcos Springflow Scenarios Evaluated in Stella 4-121 4-30: Total Fountain Darters within Representative Reaches of the San Marcos System 4-122 4-31: Low, Moderate, and High Nine-year Rolling Averages (Total San Marcos Springflow) for Phase I package (Top) and No Action Baseline (bottom) Modeled Scenarios 4-124 4-32: Low, Moderate, and High Nine-year Rolling Averages of the No Action Baseline 4-124 4-33: Total Fountain Darters in the San Marcos System for the Phase I Package – San Marcos System 4-126 4-34: Stella