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Introduction

The Edwards Aquifer in south-central Texas is one of the most productive karst aquifers in the nation. Covering an area about 180 miles long and from 5 to 40 miles wide (see Figure 1-1), it is the primary source of drinking water for over 2.3 million people in San Antonio and its surrounding communities. The aquifer also supplies irrigation water to thousands of farmers and livestock operators in the region, which can account for as much as 30 percent of the total annual water withdrawals from the aquifer system. The Edwards Aquifer has extremely high yield wells and springs, with large volumes of groundwater being transported through the system on the order of days. Thus, the aquifer responds quickly both to rainfall events and to withdrawals, such as pumping for irrigation and water supply. The region has suffered periodically from droughts (most recently 2010-2014) that can be severe enough to reduce or halt flow at the major spring outlets. Indeed during the “drought of record” in the 1950s, flows at Comal Springs ceased for four months. If such reductions in spring flow were to recur, the results could be catastrophic to the organisms living in the Edwards Aquifer and its springs.

The two largest springs emanating from the Edwards Aquifer—Comal Springs in New Braunfels and San Marcos Springs in San Marcos—are home to a number of endemic fish, amphibians, insects, and plants found nowhere else in the world. Because of the potential for reduced spring flow during drought, eight of these species are listed as threatened or endangered under the federal Endangered Species Act (ESA): the fountain darter, the San Marcos gambusia (presumed extinct), the Texas blind salamander,

the San Marcos salamander, the Comal Springs dryopid beetle, the Comal Springs riffle beetle, the Peck’s Cave amphipod, and Texas wild rice.

To protect the ESA-listed species, the Edwards Aquifer Authority (EAA) and four other local entities have created a 15-year Habitat Conservation Plan as part of their Incidental Take Permit under the ESA. The EAA is a regional government body tasked with managing domestic, industrial, and agricultural withdrawals from the Edwards Aquifer while maintaining spring flows at quantities that can support recreation and the ESA-listed species. The EAA implements the Habitat Conservation Plan, which the U.S. Fish and Wildlife Service (FWS) finalized and approved in 2013 after a years-long development process. Given the complexities of the Habitat Conservation Plan, in 2013 the EAA requested the input of the National Research Council (NRC) during implementation of the plan. This report is the second product of a three-phase study to provide advice to the EAA on various scientific aspects of the Habitat Conservation Plan that will ultimately lead to improved management of the aquifer. The first report (NRC, 2015) provides a comprehensive description of the hydrology and ecology of the Edwards Aquifer and its spring systems. It also describes in

detail the events that led to the creation of the Habitat Conservation Plan and the plan’s many elements. The reader is referred to Chapter 1 of that report for more in-depth information on these topics. A cursory summary is presented below.

THE EDWARDS AQUIFER

Hydrology and Climate

The Edwards Aquifer is a highly productive karst aquifer in south-central Texas. As shown in Figure 1-1, the contributing and recharge zones lie to the north, while pumping and artesian wells occur largely to the south. The largest area, the contributing zone (5,400 square miles), is where rainfall lands and is directed by streams toward the recharge zone. The recharge zone (approximately 1,250 square miles) is where precipitation percolates and flows into the groundwater to replenish the aquifer. In the artesian zone (2,650 square miles), the groundwater is under confined conditions, such that pressure levels in the aquifer cause the water to rise to elevations above the top of the aquifer. In such areas, groundwater flow from the aquifer to the land surface occurs in the form of springs and seeps. At least six springs occur within the artesian zone, including the two largest in Texas, the San Marcos and Comal Springs. Comal and San Marcos Springs are located within the San Antonio segment of the Edwards Aquifer, which spans approximately 3,600 square miles and is the focus of the Habitat Conservation Plan and this report. The karstic nature of the Edwards Aquifer, which is characterized by complex groundwater flow through such features as fractures, caves, and sinkholes, makes the aquifer vulnerable to potential surface water contamination.

The climate in the Edwards Aquifer region is characterized by significant spatial and temporal variability. Across the region, annual precipitation ranges from approximately 22 inches in the west to over 34 inches in the east. The mean annual precipitation for San Antonio from 1934 through 2013 was approximately 30.38 inches, although this varied annually by as much as 20 inches. Thus, it is not unusual for the Edwards Aquifer region to experience periods of high rainfall (in excess of 40 inches per year) separated by periods of drought. Evapotranspiration (unhindered vegetative rate) along the Edwards Aquifer region is similarly variable, ranging from more than 60 inches per year in the western extent to 30 inches per year in the eastern extent (Scanlon et al., 2005). However, recharge of the Edwards Aquifer occurs primarily via rapid, focused precipitation events entering the aquifer through exposed karst features within surface-exposed limestone, which lessens the role of evapotranspiration. Climate change scenarios suggest that, over the long term, precipitation in the region is ex-

pected to decrease and evapotranspiration is expected to increase (Loáiciga et al., 2000; Mace and Wade, 2008; Darby, 2010). Combined with an anticipated population increase and the associated increased demands on water resources, these factors suggest that the Edwards Aquifer is likely to become more stressed in the future.

Variations in climate in the Edwards Aquifer region are manifested in the variable nature of the aquifer’s water budget. From 1934 to 2012, the median¹ annual recharge was 556,900 acre-ft,² with a range from 43,700 acre-ft during the drought of record in the 1950s to 2,486,000 acre-ft in 1992 (EAA, 2013). Edwards Aquifer discharge is composed of spring flows and consumptive use through wells. Total annual discharge from six of the most significant springs in the region monitored between 1934 and 2012 varied from 69,800 acre-ft in 1956 to 802,800 acre-ft in 1992, with a median annual discharge of 383,900 acre-ft (EAA, 2013). Well discharge estimates during the same period ranged from a low of 101,900 acre-ft in 1934 to a high of 542,400 acre-ft in 1989, with a median annual discharge of 327,800 acre-ft.

Ecology

Several species are endemic to the springs and river systems flowing from the Edwards Aquifer, including a variety of submersed aquatic vegetation (SAV), such as Texas wild rice; several fish, including the fountain darter; amphibians, such as the Texas blind salamander; and a variety of invertebrates. All species in the system depend on adequate spring flow, such that reduced flow in Comal and San Marcos Springs has periodically resulted in the intermittent loss of habitat and decreased populations. This loss of habitat from reduced flow is the main reason that eight species have been listed for protection under the federal Endangered Species Act (ESA) (see Table 1-1). Other threats to these species include increased competition and predation from invasive species, direct or indirect habitat destruction or modification by humans (e.g., recreational activities and reservoir construction), and other factors, such as high nutrient loading and bank erosion, that negatively affect water quality and habitat (USFWS, 1996).

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¹ Note that the Committee recommends that means, not medians, be used in future reports on the water budget, including the Hydrologic Data reports from which this information was drawn.

² An acre-foot is the amount of water necessary to cover one acre of land with one foot of water. One acre-foot equals 1,233 cubic meters (m³) of water.

TABLE 1-1 Common and Scientific Names of Species Proposed for Coverage Under the Edwards Aquifer Habitat Conservation Plan and Their Status According to the Endangered Species Act

*Listed as under review by the USFWS

**Listed as undefined status by the USFWS

HABITAT CONSERVATION PLAN

The ESA, which in this case is enforced by the U.S. Fish & Wildlife Service (FWS), protects the listed species from actions that could jeopardize their continued survival. Most relevant to the EAA, the law prohibits the “take” of such species, which the ESA defines to mean “harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect, or to attempt to engage in any such conduct.” The law also allows certain entities to apply for and receive an Incidental Take Permit, which defines the number of animals that can be “taken” by certain activities (such as groundwater pumping). In order for an applicant to receive such a permit, it must develop a Habitat Conservation Plan (HCP).

The HCP for the Edwards Aquifer took years to create and required the involvement of many parties (see NRC, 2015 for details). It was finally submitted by the EAA to the FWS in 2012, after which an Incidental Take Permit was issued. The permit will last 15 years, from March 18, 2013, until March 31, 2028. The five official Permittees are the EAA; the City of San Antonio, acting through the San Antonio Water System; the City of San Marcos; the City of New Braunfels; and Texas State University. All five have responsibilities under the HCP to implement minimization and mitigation measures that will protect the listed species and their habitat. The minimization and mitigation measures that make up the HCP include

(1) four spring flow protection measures, and (2) measures designed to maintain and restore the habitat of ESA-listed species at both Comal and San Marcos Springs. A complete list of the measures can be found in NRC (2015) or the HCP itself (EARIP, 2012). The discussion below focuses on the specific measures that are evaluated, in this report, for their ability to provide benefits to the listed species.

The four spring flow protection measures were designed to provide additional water during drought and include (1) critical period management, (2) regional water conservation, (3) a voluntary irrigation suspension program, and (4) aquifer storage and recovery. Critical period management refers to reductions in permitted discharges when the spring flow at Comal Springs and water levels at reference well J-17 fall below certain levels. To offset the risks to listed species under these conditions, the HCP instituted a new stage, Stage V, which would mandate reductions in pumping of 44 percent. The Regional Water Conservation Program builds upon the demand management already being conducted by the City of San Antonio. It is envisioned that new municipal conservation activities can save approximately 10,000 acre-ft/year (12.33 million m³/year). The Voluntary Irrigation Suspension Program Option (VISPO) targets the 30 percent of annual Edwards Aquifer pumping that is withdrawn for irrigation. VISPO relies on permitted irrigators relinquishing their pumping rights when well levels and spring flows drop below certain triggers; it is intended to conserve another 40,000 acre-ft/yr (49.32 million m³/year). Finally, the San Antonio Water System (SAWS) runs an aquifer storage and recovery (ASR) operation in the Carrizo Aquifer that will be expanded and is predicted to make the greatest contribution to overall Edwards Aquifer water savings (as much as 100,000 acre-ft/year or 123.3 million m³/year).

Beyond spring flow protection measures, there are a variety of minimization and mitigation measures designed to maintain and restore the habitat of ESA-listed species at both Comal and San Marcos Springs. The measures that are evaluated in this report include aquatic vegetation restoration (including removal of invasive plant species and replanting of native species), sediment management in the spring and river systems, and dissolved oxygen management in Landa Lake.

Other programs found within the HCP that were the subject of the first report (NRC, 2015) and receive further attention in this report include water quality and biological monitoring of the aquifer and spring systems; improving the hydrologic model for the Edwards Aquifer; the creation of predictive ecological models for Comal and San Marcos Springs; and the Applied Research Program, which has been used to fund individual research projects to study the ecological dynamics within the Comal and San Marcos Spring systems. A brief overview of the first report is provided below.

THE EAA REQUESTED STUDY

In late 2013, the EAA formally requested the involvement of the NRC to provide advice on the many different scientific initiatives under way to support the HCP. An expert committee of the National Academies was asked to focus on the adequacy of the scientific information being used to, for example, (1) set biological goals and objectives, (2) determine what minimization and mitigation measures to use and their effectiveness; and (3) make decisions about the transition from Phase 1 to Phase 2 of the HCP. The study is being conducted from 2014 to 2018 and will produce three reports.

Phase 1 of National Academies Study

The Committee’s first report (NRC, 2015) was released in late February 2015 and addressed four programs within the HCP: hydrologic modeling, ecological modeling, biological and water quality monitoring programs, and the Applied Research Program. In general, the report was complimentary of the efforts of the EAA and its partners in implementing the HCP and these four programs in particular, while at the same time identifying areas that could be improved upon.

Within the hydrologic modeling arena, which has been ongoing for decades, the Committee recommended devoting future resources to a single model that incorporates the best concepts from existing models, rather than developing two “competing” models. It suggested that whatever model is selected should have features that advance the conceptual model of the system, such as telescoping meshes to accommodate shorter time scales and features for representing conduits and barriers. The Committee also stressed the need to quantitatively assess and present model uncertainty in formal EAA documents. It mentioned several techniques for doing this, including conducting more explicit sensitivity analysis; validating the groundwater model by testing its predictive abilities using data from a time period not included in the model calibration; using additional calibration and validation metrics; using PEST predictive uncertainty analysis; using the ensemble method; and having confidence intervals presented with all modeling results.

Unlike the hydrologic modeling, the ecological model was new to the HCP; thus the Committee recommended creation of a conceptual model to help determine the most important processes for a model to encompass and to show the links between flow, species populations, and other important parameters. The initial species targets of the ecological model were fountain darter and SAV because of limited data and information about the other listed species. The Committee also stressed the importance of updating the habitat suitability analysis for Texas wild rice and of developing a much

deeper understanding of the life history of the Comal Springs riffle beetle prior to including it in any ecological model.

With respect to the water quality and biological monitoring programs, the Committee was complimentary of the work that has been ongoing since 2000, which is now even more comprehensive as a result of the HCP. It noted that, because none of the sampling locations were selected using randomization procedures, results from the monitoring program are not representative of the entire spring and river systems and cannot provide system-wide estimates of population densities of target species. Enhanced sampling for nutrients and the development of new quantitative sampling methods for the Comal Springs riffle beetle were recommended.

The Committee suggested several new studies as well as programmatic issues that could improve the Applied Research Program. Examples of the latter include creating a more transparent process for prioritizing and funding Applied Research projects that includes stakeholder involvement and peer review; having greater competition and collaboration with outside scientific experts through open and widely disseminated solicitations for research; and offering some longer (e.g., two- to five-year) projects in order to maximize interest and collaboration from the region’s leading researchers.

The Committee’s first report closed with several overarching issues, including the need for more formal integration and database creation to enable clear explanation of the many sets of results emanating from the monitoring, modeling, and research efforts; the need to monitor the performance of minimization and mitigation measures currently being implemented; and the need for more formal and rigorous statistical analyses of laboratory and field data. Finally, it stressed the importance of considering various worst case scenarios as the HCP nears the end of its 15-year term.

After the release of NRC (2015), the EAA went through a lengthy process to determine how to implement the recommendations of the Committee. A formal document (EAA, 2015), including a prioritization matrix, was created by the newly formed Recommendations Review Work Group (RRWG). This document, the “Implementation Report,” responded to every recommendation made by placing it into one of the following categories: (1) Done, (2) Continual, or (3) In Progress. The recommendations were also categorized as (4) To Be Implemented with No Budget Impact; (5) To Be Determined with Budget Impact; (6) To Be Determined If Implemented and Prioritized by Working Groups (Water Quality, Biological Monitoring, Applied Research); and (7) No, Not Recommended for Implementation. Not all categories are mutually exclusive. The responses of the RRWG are referred to periodically in all of the subsequent chapters when discussing how the EAA and others have responded to NRC (2015). While the Committee applauds the RRWG effort and the creation of the Implementation Report, it is not clear that current and future project plans and timelines

will allow for the time and resources needed to address the recommendations in NRC (2015). The Committee recommends that project schedules be periodically revised to build in the time and resources needed to focus on implementing the recommendations from National Academies reports.

Phase 2 of National Academies Study

The statement of the task for the second phase of the National Academies review is given in Box 1-1. With respect to evaluating the progress and modifications implemented as a result of the Committee’s first report (task no. 1), it is not our intent to exhaustively review all programs and list all recommendations given previously in NRC (2015). Rather, the relevant sections of Chapters 2, 3, 4, and 5 focus on specific issues where additional information or clarification may be helpful in improving the programs. The primary focus in this report is to help develop questions that both the hydrologic and ecological models can be used to answer, and to evaluate implementation of the minimization and mitigation measures that are being used to protect and restore habitat and protect flow. The question of

whether these measures are sufficient and necessary to achieve the objective of ensuring survival of the listed species will be answered in the third and final National Academies report.

Hydrological Model

Tasks 1 and 3 in the Statement of Task (Box 1-1) pertain to the hydrologic modeling efforts that have been ongoing for some time in the Edwards Aquifer region. The current groundwater model for the Edwards Aquifer is a finite difference model based on MODFLOW that has been in development since 2000. (It should be noted that a finite element model of the aquifer was created during 2014 but it is not being developed further.) The major goal for the model is to be able to predict groundwater levels and spring flows under future hydrologic conditions, such as climate change and droughts. In particular, the model will be used to determine whether the four spring flow protection measures of the HCP can maintain flows at Comal and San Marcos Springs above levels critical to the listed species for sufficient durations.

Ecological Model

The ecological modeling described in the HCP has been under development since 2013 and is the subject of a short report from this Committee, released in June 2016 (NASEM, 2016; see Appendix A). According to the HCP, the two primary purposes for developing predictive ecological models are to identify and describe ecological responses of the listed species in the Comal and San Marcos Spring systems to various environmental factors and to predict and quantify impacts of various activities, including groundwater withdrawal, recreation, habitat restoration, etc., on these ecosystems and associated species. Mechanistic simulation models of moderate complexity were developed to simulate and predict the responses of fountain darter and SAV to changes in flow and water quality in the Comal and San Marcos Spring systems. The SAV model is still in the early stage of development, and the plan is for it to simulate the ecological processes of plant growth, mortality, and dispersal of multiple species on a spatial grid. The fountain darter model is further along in its development, with a functioning version now available. The fountain darter model is individual-based and uses the same spatial grid as the SAV model. Processes of growth, reproduction, movement, and mortality are represented for each individual fish. The spatial scale of both models is currently on the order of 1 m² with time steps ranging from hours or days. One goal for the future is to link the SAV and fountain darter models so that vegetation habitat in the fountain darter model also responds to flow and environmental variation, and ultimately

to have the ecological models use the outputs of the groundwater model, so that simulations can be conducted for integrated surface and groundwater systems (EARIP, 2012). This report’s treatment of the ecological modeling efforts directly responds to Tasks 1 and 3 in the Statement of Task.

Biological Monitoring

Task 2 in the Statement of Task specifically focuses on the biological and water quality monitoring programs of the HCP. A comprehensive biological monitoring plan was established by the EAA in 2000 to gather baseline and critical period data to fill important gaps in the ecological condition of the Comal and San Marcos spring and river ecosystems. This monitoring is ongoing during the 15-year term of the Incidental Take Permit in order to provide a means of monitoring changes in habitat availability and the population abundance of the listed species. The comprehensive monitoring plan increases in both frequency and the number of parameters examined as spring discharge falls below specific levels. The current program monitors the following components:

• Aquatic vegetation mapping, including Texas wild rice
• Fountain darter and fish community sampling
• San Marcos salamander sampling
• Comal Springs riffle beetle monitoring
• Comal Springs invertebrate sampling
• Comal Springs salamander sampling

A final goal of the biomonitoring program is to provide information to effectively determine whether the conservation measures are achieving the biological goals and objectives set forth in the HCP.

Water Quality Monitoring

Water quality monitoring has been in place in the Comal and San Marcos Spring systems for more than 40 years. The goals of the current program as it relates to the HCP are to detect water quality impairments that may negatively impact the listed species. Each year EAA monitors the quality of water in the Edwards Aquifer by sampling approximately 80 wells, eight surface water sites, and major spring groups across the region, including the Comal and San Marcos Springs. The program also includes sampling of stormwater runoff. Water samples are routinely analyzed in the field for selected water quality parameters (i.e., temperature, pH, conductivity, and alkalinity) and in the laboratory for common major ions, metals, total dissolved solids, hardness, bacteria, and nutrients. Many of the

samples are also analyzed for semivolatile organic compounds and volatile organic compounds as well as pesticides, herbicides, and polychlorinated biphenyls.

Applied Research Program

As noted in Task 1 of the Statement of Task, the Committee continues to review the Applied Research Program, which was created by the HCP to (1) fill gaps in knowledge about particular listed species, (2) increase understanding of key processes that affect their population dynamics, and (3) provide data and information that can be used to parameterize and validate the ecological models. The overall goal of the program is to generate useful information during Phase 1 of the HCP to be able to make well-informed decisions about the overall direction of the HCP during Phase 2. Projects to date have been evenly split between species for which there is greater knowledge, like the fountain darter and Texas wild rice, and those for which less information is available, including SAV, the Comal Springs riffle beetle, and most of the other covered species. Critical to the recovery and protection of all aquifer species is knowledge of the species-specific demography and ecology, including knowledge of natural population fluctuations. Much of the research conducted under the Applied Research Program has been to better understand the ecological dynamics of the listed species under low flow conditions. The 2016 research projects are devoted exclusively to the Comal Springs riffle beetle.

Spring Flow Protection Measures

Task 4 in the Statement of Task brings a new topic under the Committee’s purview, namely the ability of certain minimization and mitigation measures to provide benefits to the listed species. The four spring flow protection measures that are evaluated include the Voluntary Irrigation Suspension Program Option, the Regional Water Conservation Program, the Aquifer Storage and Recovery program of SAWS, and emergency withdrawal reductions during Stage V Critical Period Management. Each of these four measures is intended to contribute, in a cumulative fashion, to maintaining an adequate level of continuous spring flow during a repeat of the drought of record conditions (EARIP, 2012).

Habitat Restoration Measures

Beyond flow protection measures, there are as many as 29 other measures within the HCP aimed at restoring and improving the habitat of the listed species. Those that are considered in depth in this report fall into the

following categories: native aquatic vegetation restoration, sediment management, and dissolved oxygen management. The measures designed to restore native vegetation include Texas wild rice enhancement and restoration in the San Marcos system (HCP section 5.3.1, 5.4.1); aquatic vegetation restoration and maintenance in both the Comal and San Marcos systems (non-native removal, native reestablishment) (5.2.2, 5.3.8, 5.4.3, 5.4.12); and management of floating vegetation mats and decaying vegetation and litter removal in both spring systems (5.2.4, 5.3.3, 5.4.3). Sediment management is focused to two areas in the San Marcos system: Sewell Park and Sessom Creek sand bar removal. Dissolved oxygen management is ongoing primarily in Landa Lake in the Comal system.

REPORT ROADMAP

Chapter 2 of this report addresses the hydrologic modeling of the Edwards Aquifer. It reviews how the EAA has responded to the recommendations in the first report regarding uncertainty analyses, recharge estimates, and how to represent features such as conduits and shorter time steps. It also poses questions that the hydrologic model could be used to answer as the HCP transitions from Phase 1 to Phase 2. Chapter 3 describes the ecological modeling for Comal and San Marcos Springs, focusing on the initial modeling efforts for the fountain darter and SAV. It builds on a short interim report (NASEM, 2016) released in June 2016 that dealt with the model structure and issues to keep in mind as the model is finalized (see Appendix A). The chapter finishes with scenarios that the ecological model should be used to address, which can either be diagnostic based (e.g., varying process rates) or evaluative (e.g., running the EAA’s so-called bottom-up package of the four spring flow protection measures).

Chapter 4 updates the Committee’s review of the comprehensive water quality monitoring program and biomonitoring program. It considers the adequacy of both programs and makes recommendations for what should continue to be sampled as the HCP moves forward. Chapter 5 discusses the Applied Research Program, including how the EAA has responded to recommendations in the first report. Chapter 6 comprehensively evaluates the four spring flow protection measures and the select habitat restoration measures of the HCP, considering how they should be implemented and monitored to be of maximum benefit to the listed species.

Each chapter ends with conclusions and recommendations that synthesize more technical and specific statements found within the body of each chapter. The most important conclusions and recommendations are repeated in the report summary. It should be noted that substantial information provided in the first report, such as the descriptions of each program, definitions of terms, and rationale for key recommendations,

is not repeated in this report. The reader is referred to NRC (2015) for such details.

REFERENCES