Environmental Flows Recommendations Report Final Submission to the Guadalupe, San Antonio ...

427 Pages·2011·14.74 MB·English

by  Linda Whitaker

Environmental Flows Recommendations Report
Final Submission to the Guadalupe, San Antonio, Mission, and Aransas Rivers and
Mission, Copano, Aransas, and San Antonio Bays Basin and Bay Area Stakeholder
Committee, Environmental Flows Advisory Group, and Texas Commission on
Environmental Quality

Guadalupe, San Antonio, Mission, and Aransas Rivers and
Mission, Copano, Aransas, and San Antonio Bays
Basin and Bay Expert Science Team

March 1, 2011

i
Table of Contents

Acknowledgements

1. Preamble ........................................................................................................................ 1.1
1.1 Senate Bill 3 Environmental Flows Process.................................................... 1.1
1.1.1 Environmental Flows Advisory Group (EFAG) ..................................... 1.1
1.1.2 Science Advisory Committee (SAC) ........................................................ 1.1
1.1.3 Basin and Bay Area Stakeholder Committee (BBASC) .......................... 1.1
1.1.4 Texas Commission on Environmental Quality (TCEQ) .......................... 1.2
1.2 Guadalupe, San Antonio, Mission, and Aransas Rivers and Mission, Copano,
Aransas, and San Antonio Bays Basin and Bay Expert Science Team (GSA
BBEST) .............................................................................................................. 1.3
1.2.1 Membership............................................................................................. 1.3
1.2.2 GSA BBEST Charge ................................................................................ 1.3
1.3 Sound Ecological Environment ....................................................................... 1.5
1.3.1 Sound Ecological Environments – Riverine ........................................... 1.6
1.3.2 Sound Ecological Environments – Estuarine ......................................... 1.6
1.4 Introduction to Environmental Flows Recommendations Report ............... 1.9

2. Overview of Watersheds and Bays .............................................................................. 2.1
2.1 Guadalupe River Basin..................................................................................... 2.1
2.1.1 Summary of Water Quality Characteristics ............................................ 2.3
2.1.2 Electric Cooling Water ........................................................................... 2.4
2.1.3 Canyon Reservoir and the Guadalupe Hydroelectric System................. 2.4
2.2 San Antonio River Basin .................................................................................. 2.7
2.2.1 Hydrology ............................................................................................... 2.7
2.2.2 Biology .................................................................................................... 2.9
2.2.3 Physical Processes ................................................................................ 2.10
2.2.4 Water Quality ........................................................................................ 2.11
2.3 San Antonio Bay .............................................................................................. 2.12
2.4 San Antonio – Nueces Coastal Basin ............................................................. 2.14
2.4.1 Water Quality ........................................................................................ 2.15
ii
2.4.2 Hydrology ............................................................................................. 2.15
2.5 Mission, Copano, and Aransas Bays ............................................................. 2.16

3. Instream Flow Analyses ............................................................................................... 3.1
3.1 Geographic Scope.............................................................................................. 3.2
3.1.1 Streamflow Gaging Stations ................................................................... 3.2
3.1.2 Selection of Flow Regime Recommendation Locations .......................... 3.2
3.1.2.1 Hydrology ................................................................................... 3.3
3.1.2.2 Biology ........................................................................................ 3.6
3.1.2.3 Water Quality .............................................................................. 3.7
3.1.2.4 Geomorphology .......................................................................... 3.8
3.1.2.5 Water Availability and Supply Planning .................................... 3.8
3.1.2.6 Geographic Interpolation ............................................................ 3.8
3.2 Hydrology-Based Environmental Flow Regimes ......................................... 3.11
3.2.1 Hydrographic Separation ..................................................................... 3.13
3.2.2 Period of Record ................................................................................... 3.15
3.2.3 Season Selection.................................................................................... 3.22
3.2.4 Flow Regime Components .................................................................... 3.22
3.2.4.1 Subsistence Flows ..................................................................... 3.22
3.2.4.2 Base Flows ................................................................................ 3.22
3.2.4.3 High Flow Pulses and Overbank Flows .................................... 3.23
3.2.5 Initial Hydrology-Based Flow Regimes ................................................ 3.24
3.3 Biology Overlay ....................................................................................... 3.25
3.3.1 Description of Methodologies and Assumptions................................... 3.25
3.3.1.1 Natural Flow Paradigm ............................................................. 3.25
3.3.1.2 Quantification of Flow Regime Components ........................... 3.26
3.3.1.3 Linking the Hydrologic Regime to Riverine Habitat ................ 3.28
3.3.2 Development of Habitat Guilds and Selection of Focal Species .......... 3.29
3.3.3 Habitat Guild Suitability in terms of Physical Habitat Attributes ........ 3.30
3.3.3.1 Habitat Suitability Criteria (HSC) ............................................ 3.30
3.3.3.2 Selection of Final Focal Species and Habitat Guilds ................ 3.31
3.3.3.3 Habitat Suitability Curve Development .................................... 3.31
iii
3.3.3.4 Key Life History Characteristics of Guild Species ................... 3.34
3.3.3.5 Development of Guild Specific Habitat Suitability Curves ...... 3.38
3.3.4 Other Important Species ....................................................................... 3.46
3.3.5 Estimating Habitat Guild Availability as a Function of
Discharge Ranges ................................................................................. 3.46
3.3.5.1 Physical Habitat Modeling ........................................................ 3.47
3.3.5.2 Use of Existing Site-specific Habitat Modeling Results........... 3.49
3.3.6. Use of Historical Cross Section Data to Develop Habitat
Relationships ....................................................................................... 3.52
3.3.7 Comparative Cross Section Methodology ............................................ 3.58
3.3.7.1 Habitat versus Flow Relationships for Habitat Guilds ............. 3.59
3.3.7.2 Sensitivity of Habitat versus Discharge Curves to
Habitat Guild HSC .................................................................... 3.73
3.4 Water Quality Overlay ................................................................................... 3.76
3.5 Geomorphology Overlay ................................................................................ 3.81
3.5.1 Geomorphology (Sediment Transport) ................................................. 3.81
3.5.2 Study Locations ..................................................................................... 3.82
3.5.3 Frequency Curves ................................................................................. 3.82
3.5.4 Discharge Rating Curves ...................................................................... 3.86
3.5.5 Sediment Rating Curves ........................................................................ 3.88
3.5.6 Hydrologic Time Series......................................................................... 3.90
3.5.6.1 Effective Discharge Calculations .............................................. 3.97
3.5.6.2 Effective Discharge Results ...................................................... 3.97
3.5.6.3 San Antonio River at Goliad ..................................................... 3.99
3.5.6.4 Guadalupe River at Cuero ....................................................... 3.103
3.5.6.5 Summary Points ...................................................................... 3.106
3.5.6.6 Conclusions ............................................................................. 3.107
3.6 Riparian Biological Overlay......................................................................... 3.109
3.6.1 Overview of Approach ........................................................................ 3.109
3.6.2 Riparian Definition and Importance ................................................... 3.109
3.6.3 Exotic Species ..................................................................................... 3.114
3.6.4 Flow-Ecology Relationships among Physical Processes
and Riparian Habitat .......................................................................... 3.116
iv
3.6.5 Flow Regimes and Associated Environmental Relationship
to Riparian Systems............................................................................. 3.118
3.6.6 Flow Variations and Timing ............................................................... 3.119
3.6.7 Riparian Characterization for Guadalupe, San Antonio,
and San Antonio-Nueces Coastal Basins ............................................ 3.121
3.6.8 Riparian Corridors in the Guadalupe-San Antonio Basin
and San Antonio–Nueces Coastal Basin (Mission River): Sound
Ecological Environment...................................................................... 3.138
3.6.9 Flow Regime Recommendations for Riparian Overlay ...................... 3.142

4. Freshwater Inflow (FWI) Analyses ............................................................................. 4.1
4.1 Effects of Freshwater Inflow on Estuarine Ecosystems ................................ 4.1
4.1.1 Dynamics of Estuarine Freshwater Inflow Regimes ............................... 4.2
4.1.1.1 Salinity Gradients........................................................................ 4.3
4.1.1.2 Nutrient Supply ........................................................................... 4.4
4.1.1.3 Sediment Supply ......................................................................... 4.4
4.1.2 Physiography and Ecology of Guadalupe-San Antonio and Mission-
Aransas Estuaries ................................................................................... 4.4
4.1.3 Dynamics of FWI Regimes ...................................................................... 4.5
4.1.4 Response of Delta Low-salinity Marsh Communities to Freshets .......... 4.6
4.1.5 Life Cycles of Estuarine Species and Linkage to Freshets ..................... 4.6
4.1.6 Inflow Stress Produced under Low Flow or Drought Conditions .......... 4.7
4.1.7 Conclusion .............................................................................................. 4.8
4.2 Hydrology and Salinity ................................................................................... 4.11
4.2.1 Historical Inflows and Salinity Patterns ............................................... 4.11
4.2.2 Salinity Simulations and Prediction...................................................... 4.19
4.3 Key Bay Species/Habitat and Responses to Salinity .................................... 4.30
4.3.1 Focal Species and Rationale for Selection ........................................... 4.30
4.3.1.1 Eastern Oyster (Crassosterea virginica) ................................... 4.31
4.3.1.2 Atlantic Rangia (Rangia cuneata) and Brown Rangia (Rangia
flexuosa) .................................................................................... 4.33
4.3.1.3 White Shrimp (Litopenaeus setiferus) ...................................... 4.37
4.3.1.4 Blue Crabs (Callinectes sapidus) .............................................. 4.41
4.3.2 Selection of Fixed Habitat Target Areas .............................................. 4.56
v
4.3.2.1 Eastern Oysters ......................................................................... 4.56
4.3.2.2 Rangia ....................................................................................... 4.57
4.3.3 Focal Species – Other Important Species ............................................. 4.62
4.3.3.1 Guadalupe Delta Plant Species as Indicators of FWI Effects ... 4.62
4.4 Salinity Zone Methodology ............................................................................ 4.65
4.4.1 The Methodology Utilized for Guadalupe and
Mission-Aransas Estuaries ................................................................... 4.65
4.5 Analyses for Focal Species.............................................................................. 4.88
4.5.1 Salinity Zone Application – Guadalupe Estuary ................................. 4.88
4.5.1.1 Oysters, Guadalupe Estuary ...................................................... 4.89
4.5.1.2 Rangia, Guadalupe Estuary ....................................................... 4.93
4.5.2 Salinity Zone Application – Mission-Aransas Estuary ....................... 4.102
4.5.2.1 Oysters, Aransas Bay .............................................................. 4.106
4.5.2.2 Oysters, Copano Bay .............................................................. 4.108
4.5.2.3 Rangia, Copano Bay ............................................................... 4.110
4.5.3 Other Focal Species Analyses ............................................................. 4.115
4.5.3.1 White Shrimp (Motile Species) Analysis ............................... 4.115
4.5.3.2 Blue Crab (Motile Species) Analysis ...................................... 4.128
4.6 Synthesis of Biology-Based Inflow Regime Components
for the Guadalupe and Mission-Aransas Estuaries ................................... 4.134

5. Integration of Instream Flow and Estuary Inflow Regimes ..................................... 5.1
5.1 Comparison of Initial Estuary Inflow to Instream Flow Regimes ............... 5.1
5.2 Nutrient Considerations – Estuarine .............................................................. 5.9
5.2.1 Nitrogen Cycling in Coastal Ecosystems .............................................. 5.11
5.2.2 Land Use/Land Cover ........................................................................... 5.12
5.2.3 Nutrient and organic matter export from the San
Antonio and Guadalupe river watersheds to San Antonio Bay ............ 5.12
5.2.4 Estuarine Monitoring within the Mission-Aransas National
Estuarine Research Reserve ................................................................. 5.20
5.3 Sediment Considerations ................................................................................ 5.25
5.3.1 Sediment Loading to Guadalupe Bay ................................................... 5.25
5.3.2 Sediment Loading Related to Instream Pulse Flows ............................ 5.26

vi
5.4 Effects on Initial Freshwater Inflow and Instream Flow Regimes............. 5.27

6. Environmental Flow Regime Recommendations ....................................................... 6.1
6.1 Environmental Flow Regime Summaries ....................................................... 6.2
6.1.1 Subsistence Flows ................................................................................. 6.19
6.1.2 Base Flows ............................................................................................ 6.19
6.1.3 High Flow Pulses .................................................................................. 6.19
6.1.4 Overbank Flows .................................................................................... 6.20
6.1.5 Definition of Hydrologic Condition (Wet/Average/Dry) ...................... 6.20
6.1.6 Estuarine Inflow Regime Summaries .................................................... 6.21
6.1.7 Attainment Goals for Estuarine Inflow Recommendations ................... 6.24
6.2 Comparisons to Water Rights Permits ......................................................... 6.25
6.3 Comparison of GSA BBEST Estuary Recommendations
to Texas State Methodology ........................................................................... 6.26
6.4 Example Applications of Flow Regime Recommendations ......................... 6.30
6.4.1 Subsistence Flows ................................................................................. 6.30
6.4.2 Base Flows ............................................................................................ 6.30
6.4.3 High Flow Pulses .................................................................................. 6.30
6.4.4 General Considerations ........................................................................ 6.31
6.4.5 Example Flow Regime Applications and Verification .......................... 6.31

7. Adaptive Management.................................................................................................. 7.1
7.1 Research Priorities, Data Collection, and Monitoring
Recommendations ............................................................................................. 7.2
7.1.1 Instream Flows........................................................................................ 7.2
7.1.1.1 Hydrology and Water Quality ..................................................... 7.2
7.1.1.2 Multi-disciplinary Approaches ................................................... 7.3
7.1.1.3 Biology Overlay .......................................................................... 7.4
7.1.1.4 Geomorphology Overlay ............................................................ 7.5
7.1.1.5 Riparian Vegetation Overlay ...................................................... 7.7
7.1.2 Freshwater Inflows to Bays and Estuaries ................................................ 7.8
vii
7.1.2.1 Hydrology and Salinity ............................................................... 7.8
7.1.2.2 Key Bay Species/Habitat and Responses to Salinity .................. 7.9
7.1.2.3 Nutrient Considerations ............................................................ 7.10

8. References

viii
Acknowledgements

The members of the Guadalupe, San Antonio, Mission, and Aransas Rivers and Mission,
Copano, Aransas, and San Antonio Bays Basin and Bay Expert Science Team respectfully and
gratefully acknowledge the invaluable technical and logistical support provided by the following
organizations and very capable individuals:

Texas Parks and Wildlife Department – Dan Opdyke, Lynne Hamlin, Norman Boyd, Karen
Meador, Mark Fisher, Nathan Kuhn, Wen Lee, Angela Schrift, James Tolan, John Botros, Kevin
Mayes, and Clint Robertson

Texas Water Development Board – Ruben Solis, Carla Guthrie, Mark Wentzel, Nolan Raphelt,
Mike Vielleux, Caimee Schoenbaechler, Junji Matsumoto, and Qingguang Lu

Texas Commission on Environmental Quality – Cory Horan, Chris Loft, and Gregg Easley

University of Texas Marine Science Institute – Zack Darnell, Jim McClelland

Guadalupe-Blanco River Authority – Tommy Hill, Liz Sedlacek

Texas State University – Mary Van Zant

Kennedy Resource Company – Kirk Kennedy

A special expression of gratitude is extended to the San Antonio River Authority and its
dedicated staff members including Steve Raabe, Luke Habenicht, and Linda Whitaker, who have
worked tirelessly to assemble and publish this Environmental Flows Recommendations Report.

ix
1. Preamble

1.1 Senate Bill 3 Environmental Flows Process

Senate Bill 3 (SB3) of the 80th Texas Legislature established a process for the development and
implementation of environmental flow standards applicable to major river basins and estuarine
systems across the State of Texas. As summarized in Figure 1.1-1, this process began with
selection of the Environmental Flows Advisory Group (EFAG) and reaches an interim
conclusion for each river basin and associated estuarine system upon Texas Commission on
Environmental Quality (TCEQ) adoption of rules implementing environmental flow standards.
This Environmental Flows Recommendations Report is the primary deliverable of the
Guadalupe, San Antonio, Mission, and Aransas Rivers and Mission, Copano, Aransas, and San
Antonio Bays Basin and Bay Expert Science Team (GSA BBEST) and is timely submitted in the
midst of the SB3 environmental flows process to serve as a useful technical resource.

1.1.1 Environmental Flows Advisory Group (EFAG)

The EFAG is comprised of nine members including three Texas state senators, three state
representatives, and three commissioners or board members respectively representing the TCEQ,
Texas Parks and Wildlife Department (TPWD), and the Texas Water Development Board
(TWDB). Key responsibilities of the EFAG include appointment of the Science Advisory
Committee (SAC) and Basin and Bay Area Stakeholder Committees (BBASC).

1.1.2 Science Advisory Committee (SAC)

The SAC is comprised of nine technical experts in diverse areas relevant to evaluation of
environmental flows, and has since 2009 diligently provided documented guidance to both
BBESTs and BBASCs. Guidance provided by the SAC regarding environmental flows has
addressed geographic scope, use of hydrologic data, fluvial sediment transport (geomorphology),
methodologies for establishing freshwater inflow regimes for estuaries, biological overlays,
nutrient and water quality overlays, moving from flow regimes to flow standards, lessons learned
from early BBESTs, work plans for adaptive management, methods for evaluating inter-
relationships between environmental flow regimes and water supply projects, and consideration
of attainment frequencies and hydrologic conditions. This guidance has been relied upon by the
GSA BBEST in execution of its charge and creates the general structure of this recommendations
report.

1.1.3 Basin and Bay Area Stakeholder Committee (BBASC)

BBASCs must reflect a fair and equitable balance of interest groups concerned with particular
river basins and bay systems. Interest groups represented on BBASCs include: agriculture,
recreation, municipalities, soil and water conservation districts, refining industry, chemical
manufacturing, electricity generation, commercial fishing, public interests, regional water
planning, groundwater conservation districts, river authorities, and environmental groups.
BBASCs, in turn, appoint BBESTs comprised of technical experts with knowledge of particular
river basin and bay systems and/or development of environmental flow regimes. The GSA
1.1