United States Department Ofthe Interior ~

u.s. FISH & Wll.DLIFE SERVICE United States Department ofthe Interior

FISH AND WILDLIFE SERVICE ~~0~,.,... 10711 Burnet Road, Suite 200 Austin, Texas 78758-4460 512 490-0057 FAX 490-0974

AUG 0 5 2013

Mr. Michael J. Grizer 802 CES/CL 1555 Gott St. JBSA Lackland, Texas 78236-5645 Consultation No. 02ETAU00-2013-F-0060

Dear Mr. Grizer:

Enclosed is the U.S. Fish and Wildlife Service's (Service) final biological and conference opinions for the effects of ongoing Edwards Aquifer well withdrawals by Joint Base San Antonio (JBSA) on listed threatened and endangered species pursuant to the Endangered Species Act of 1973, as amended. JBSA continues to provide leadership on conservation of endangered species and water from the Edwards Aquifer upon which they depend. Water conservation and efficiency efforts at JBSA installations provide an exemplary way of protecting the Edwards Aquifer dependent ecosystems.

If JBSA is amenable, we are available to meet and discuss opportunities for meeting ongoing conservation needs. In future communications on JBSA's use of the Edwards Aquifer, please refer to consultation number 02ETAU00-2013-F-0060. If we may be of any assistance, please contact Tanya Sommer at (512) 490 0057 extension 222.

ly,

cc: Wing Commander, JBSA Matthew Cooksey, JBSA

Table of Contents 1. Consultation history ...... 1

2. Description of the action ...... 1 Action Area ...... 3 Edwards and Trinity Aquifers and Selected Springs ...... 4 Comal Springs ...... 5 Hueco Springs ...... 6 San Marcos Springs ...... 6 Fern Bank Springs ...... 7 Proposed Conservation Measures ...... 8

3. Status of the species and environmental baseline ...... 9 a. Texas wild-rice ...... 9 Species Description and Life History ...... 9 Historic and Current Distribution ...... 10 Reasons for Decline and Threats to Survival ...... 11 Survival Needs and Recovery Criteria ...... 13 Factors affecting the species within the Action Area ...... 13 Critical Habitat ...... 14 b. Peck’s cave amphipod ...... 15 Species Description and Life History ...... 15 Historic and Current Distribution ...... 16 Reasons for Decline and Threats to Survival ...... 17 Survival Needs and Recovery Criteria ...... 18 Factors affecting the species within the Action Area ...... 18 Critical Habitat ...... 18 c. Comal Springs dryopid beetle ...... 20 Species Description and Life History ...... 20 Historic and Current Distribution ...... 21 Reasons for Decline and Threats to Survival ...... 21 Survival Needs and Recovery Criteria ...... 22 Factors affecting the species within the Action Area ...... 23 Critical Habitat ...... 23 d. Comal Springs riffle beetle ...... 25 Species Description and Life History ...... 25 Historic and Current Distribution ...... 26 Reasons for Decline and Threats to Survival ...... 26 Survival Needs and Recovery Criteria ...... 27 Factors affecting the species within the Action Area ...... 27 Critical Habitat ...... 28 e. San Marcos gambusia ...... 29 Species Description and Life History ...... 29 Historic and Current Distribution ...... 30 Reasons for Decline and Threats to Survival ...... 31 Survival Needs and Recovery Criteria ...... 32 Factors affecting the species within the Action Area ...... 32 Critical Habitat ...... 33 f. fountain darter ...... 34 Species Description and Life History ...... 34 Historic and Current Distribution ...... 34 Reasons for Decline and Threats to Survival ...... 36 Survival Needs and Recovery Criteria ...... 37 Factors affecting the species within the Action Area ...... 37 Critical Habitat ...... 39 g. San Marcos salamander ...... 40 Species Description and Life History ...... 40 Historic and Current Distribution ...... 41 Reasons for Decline and Threats to Survival ...... 41 Survival Needs and Recovery Criteria ...... 42 Factors affecting the species within the Action Area ...... 42

Critical Habitat ...... 43 h. Texas blind salamander ...... 44 Species Description and Life History ...... 45 Historic and Current Distribution ...... 45 Reasons for Decline and Threats to Survival ...... 46 Survival Needs and Recovery Criteria ...... 46 Factors affecting the species within the Action Area ...... 46 Critical Habitat ...... 47 i. Environmental Baseline Factors Shared by Species in Consultation ...... 47

4. Effects of the Action ...... 47 a. Factors to be considered ...... 48 Weather-dependent effects of the action ...... 48 Probability of drought and recurrence of drought of record (DOR) conditions ...... 49 Potential impacts of climate change ...... 49 Edwards Aquifer modeling and springflows ...... 52 b. Analysis for Effects of the Action ...... 52 i. Texas wild-rice ...... 52 Effects of action on Texas wild-rice ...... 52 Effects of action on designated critical habitat ...... 53 ii. Peck’s cave amphipod ...... 53 Effects of action on the Peck’s cave amphipod ...... 53 Effects of action on designated critical habitat ...... 56 iii. Comal Springs dryopid beetle ...... 56 Effects of action on the Comal Springs dryopid beetle ...... 56 Effects of action on designated critical habitat ...... 58 iv. Comal Springs riffle beetle ...... 58 Effects of action on the Comal Springs riffle beetle ...... 58 Effects of action on designated critical habitat ...... 60 v. San Marcos gambusia ...... 60 Effects of action on the San Marcos gambusia ...... 60 Effects of action on designated critical habitat ...... 60 vi. Fountain darter ...... 61 Effects of action on the fountain darter ...... 61 Effects of action on designated critical habitat ...... 62 vii. San Marcos salamander ...... 63 Effects of action on San Marcos salamander ...... 63 Effects of action on designated critical habitat ...... 63 viii. Texas blind salamander ...... 64 Effects of action on Texas blind salamander ...... 64

5. Cumulative Effects ...... 65

6. Biological Opinion Conclusion ...... 67

7. Incidental Take Statement ...... 69 a. Reasonable and prudent measures ...... 70 b. Terms and conditions ...... 71

8. Conference Opinion on Proposed Revisions to Critical Habitat ...... 71 Differences between current designated and proposed critical habitat for Comal Springs invertebrates ...... 72 Effects of action on proposed revision to critical habitat for Peck’s cave amphipod ...... 73 Effects of action on proposed revision to critical habitat for Comal Springs dryopid beetle ...... 73 Effects of action on proposed revision to critical habitat for Comal Springs riffle beetle ...... 73 Conference Opinion Conclusion on Proposed Critical Habitat Revisions ...... 74

9. Conservation Recommendations ...... 75

10. Re-initiation Requirements ...... 76

11. References Cited ...... 77

LIST OF TABLES

(1) Proposed Joint Base San Antonio (JBSA) Edwards Aquifer use for normal and critical period conditions

(2) General distribution of endangered and threatened species dependent on the Edwards Aquifer.

(3) Estimated Size of Populations of Comal Springs Invertebrates in Comal Springs System

(4) Incidental take calculations for Comal Spring invertebrates (at Comal Springs), fountain darter (in Comal and San Marcos River systems), and San Marcos salamander

(5) Incidental take summary for Comal Springs invertebrates, fountain darter, and San Marcos salamander

(6) A comparison of original designated and proposed revised critical habitat for the Comal Springs invertebrates

LIST OF FIGURES

(1) Action area for Joint Base San Antonio formal consultation on Edwards Aquifer use

(2) Comal Springs and Landa Lake with spring habitats supporting Comal Springs invertebrates

(3) Comal Springs as mapped by Chad Norris and others in April 2012 (Norris 2013)

(4) Simulated Comal Springs Discharge (Monthly Mean) with Historic Recharge Sequence using Edwards Aquifer Recovery Implementation Program Habitat Conservation Plan Phase I and Phase II Management

List of Abbreviations, Acronyms, and Initialisms acre-ft acre-foot, (equal to 325.85143 kilogallons) Act Endangered Species Act of 1973 AFB Air Force Base BA Biological Assessment CFR Code of Federal Regulations cfs cubic feet per second CH Critical habitat CPM Critical period management CSDB Comal Springs dryopid beetle(s) CSRB Comal Springs riffle beetle(s) CY Calendar Year DOD Department of Defense DOR Drought of Record EA RIP Edwards Aquifer Recovery Implementation Program EAA Edwards Aquifer Authority et al. et alia, and others et seq. et sequens, et sequentes; and the following one(s) FR Federal Register ft foot, feet gcpd gallons per capita per day HCP Habitat Conservation Plan JBSA Joint Base San Antonio kgal kilogallon, (1000 gallons US) m meter NBU New Braunfels Utilities NMFS National Marine Fisheries Service, NOAA Fisheries PCA Peck’s cave amphipod(s) PCE Primary constituent elements (of critical habitat) SAWS San Antonio Water System SMG San Marcos gambusia SMS San Marcos salamander(s) TAC Texas Administrative Code TBS Texas blind salamander(s) TWR Texas wild-rice USGS U.S. Geological Survey

Biological Opinion for JBSA Edwards Aquifer Use Page 1

BIOLOGICAL AND CONFERENCE OPINIONS

These biological and conference opinions are based on information in your October 16, 2012, biological assessment (provided December 5, 2012, and updated February 28, 2013), supplemental information provided by JBSA, discussions with involved parties, and other information available to us in our files. A complete administrative record of this consultation is on file in the Austin Ecological Services Field Office.

1. Consultation History

Since 1996, the Department of Defense, U.S. Air Force, and U.S. Army in the San Antonio area have coordinated with the Service on their endangered species responsibilities. On November 5, 1999, the Service issued a biological opinion for the use of the Edwards Aquifer groundwater initially at four military locations (Fort Sam Houston, Lackland AFB, Kelly AFB, and Randolph AFB). Since then, Kelly AFB has been privatized and the biological opinion covering Edwards Aquifer withdrawals by JBSA has been updated, amended, and extended through August 9, 2013.

January 11, 2008 The Service issued a five year biological opinion for JBSA’s Edwards Aquifer groundwater withdrawals; JBSA, subsequently provided annual reports;

January 31, 2012 The Service and JBSA met at Fort Sam Houston to discuss the biological assessment and upcoming formal consultation on use of the Edwards Aquifer;

September 18, 2012 The Service and JBSA met at San Marcos National Fish Hatchery and Technology Center to discuss the biological assessment;

December 5, 2012 JBSA (2012) provided the Service with a biological assessment (BA);

December 31, 2012 The Service extended the biological opinion from 2008 and incidental take statement through April 30, 2013, and commented on the BA;

February 28, 2013 JBSA provided responses to Service comments;

May 28, 2013 The Service provided JBSA with draft biological opinion;

July 11, 2013 JBSA requested extension of formal consultation to August, 9, 2013; and,

July 15, 2013 JBSA provided comments on draft biological opinion.

2. Description of the Action

Section 7 of the Act requires that all Federal agencies consult with the Service to ensure that discretionary Federal actions authorized, funded, or carried out by such agencies do not jeopardize the continued existence of any threatened or endangered species or result in the Biological Opinion for JBSA Edwards Aquifer Use Page 2 destruction or adverse modification of designated critical habitat. This biological opinion does not rely on the regulatory definition of “destruction or adverse modification of critical habitat” at 50 CFR 402.02. Instead, we have relied on the statutory provisions of the Endangered Species Act to complete the analysis with respect to critical habitat.

The Act requires each Federal agency to confer with the Service on any agency action which is likely to jeopardize the continued existence of any species proposed to be listed under the Act or result in the destruction or adverse modification of critical habitat proposed to be designated for such species. If requested by the Federal agency and deemed appropriate by the Service, a conference may be conducted in accordance with the procedures for formal consultation at 50 CFR 402.14.

This consultation deals specifically with those JBSA locations that pump water from the Edwards Aquifer. The JBSA withdraws water from the Edwards Aquifer to sustain its military missions at JBSA-Fort Sam Houston, JBSA-Lackland, and JBSA-Randolph. JBSA-Camp Bullis is in the Edwards Aquifer recharge zone and involved in Edwards Aquifer research. However, JBSA-Camp Bullis does not withdraw water from the Edwards Aquifer and its water supply is not included in this consultation. The volume and rate of water use varies at each JBSA location depending on the activities being conducted and supported. Chapter 3 of the BA provides detailed background on the history, current missions, tenant organizations, and mission partners for each of these locations.

Water withdrawal from the Edwards Aquifer under consideration in this consultation is pumped directly by JBSA from the Edwards Aquifer. Water demand at the JBSA is related to the number of people living and working on the bases. The total population for the subject JBSA locations (JBSA-Fort Sam Houston, JBSA-Randolph, and JBSA-Lackland) is currently about 103,000. The population is expected to be level for the next five years, near 100,000. The BA (BA Table 4-3) presents the historic, current, and projected population of JBSA from 2005 through 2018. The average total JBSA population for 2008–2012 was 92,784.

The 2008–2012 average Edwards Aquifer use by JBSA was 4,838 acre-feet per year. The JBSA water use per capita for this period averages about 46 gallons per capita per day (gpcd), which is significantly less than current and projected municipal per capita water use (greater than 120 gcpd) for the South Central Texas Region (HDR 2010). The State Water Plan (TWDB 2012, Table 3.4) provides the most recent estimations of per capita water use for the 40 largest cities in Texas. The 2008 residential use in these cities ranged from 60 to 159 gpcd with an average of 95 gpcd. While there are differences between JBSA locations and these cities, JBSA’s low water use is notable.

The proposed Federal action is withdrawal of groundwater from the Edwards Aquifer to support national security initiatives at JBSA. JBSA summarized their proposed action in the BA as: (1) a baseline Edwards Aquifer withdrawal rate of 12,012 acre-feet groundwater annually when the Edwards Aquifer is not in any of the five stages of critical period management, and (2) reduced groundwater withdrawal rates during periods of drought (critical period). Table 1 shows the critical period stages, percent reduction from baseline groundwater use, and monthly maximum groundwater withdrawal rates.

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The proposed Federal action is a part of the consumptive demand on the regional groundwater system that provides flow to Comal, Hueco, and San Marcos springs. From 2008 through 2011, the JBSA pumped an average of 4,786 acre-feet per year, or about 39.8 percent of its 12,012 acre-feet per year maximum. During the same period, the average total amount of groundwater pumped from the Edwards Aquifer was 406,200 acre-feet per year. The JBSA’s withdrawal averages about 1.2 percent of the total amount of groundwater withdrawn annually from the aquifer. The main effect of groundwater withdrawal on federally listed threatened and endangered species is the reduction of springflow at Comal, Hueco, and San Marcos springs. When the Edwards Aquifer groundwater levels fall: (1) total springflow is reduced, (2) springs may stop flowing (particularly those at higher elevations), (3) spring run habitat is diminished, (4) water quality is degraded, (5) flows are more variable compared to average conditions, and (6) cave-adapted species may be adversely affected should groundwater levels drop below occupied cave habitat.

The JBSA locations function like small municipalities, using water for multiple purposes. Missions may be changed, expanded, or reduced requiring an increase or decrease in water use, but JBSA water use is not to exceed 12,012 acre-feet per year. Some of these uses are discretionary, while others are nondiscretionary. Nondiscretionary water uses are those necessary to accomplish the missions and support the health and safety of resident employees and their families living on the military bases. Discretionary water uses by JBSA include water used for watering landscaping, golf courses, parade grounds and similar areas; ornamental fountains; car washing; and recreational swimming pools.

JBSA has identified 12,012 acre-feet per year from the Edwards Aquifer as its baseline groundwater supply. JBSA proposes to align its critical period management stages and withdrawal reductions with the current Edwards Aquifer Authority such that during specific stages of drought (critical period) monthly maximum withdrawals for the next 15 years will be reduced from the JBSA baseline as presented in Table 1.

San Antonio Water System (SAWS) is a purveyor of recycled water and groundwater from the Edwards Aquifer. SAWS is one of the co-permittees for an ESA section 10(a)1(B) incidental take permit for Edwards Aquifer dependent species through the Edwards Aquifer Recovery Implementation Program Habitat Conservation Plan (EARIP HCP). Any Edwards Aquifer water supplied by SAWS to JBSA will be accounted for separately and is addressed by the EARIP incidental take permit. Edwards Aquifer water originating outside of JBSA will be used and conserved according to JBSA’s Conservation Management Plan for Edwards Aquifer Water Use.

Action Area

The regulations implementing section 7(a)(2) of the Act define the action area as all areas affected directly or indirectly by the Federal action and not merely the immediate area affected by the project (50 CFR § 402.02). For the purposes of this biological and conference opinion, the action area is bounded by Bexar, Comal, and Hays counties and includes: (A) the land, wells, water infrastructure, and facilities of JBSA, (B) the contributing, recharge, and artesian zones of the Edwards Aquifer, (C) all Edwards Aquifer springs supporting federally listed species including Comal Springs, Hueco Springs, San Marcos Springs, and Fern Bank Springs, and

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(D) the waterways supplied by these springs where federally listed species occur, including the Comal River and upper San Marcos River (See Figure 1). The action area presented in the Section 2 of the BA includes the Edwards Aquifer. We identify the Edwards Aquifer in Bexar, Comal, and Hays counties as the subset of the Edwards Aquifer that may be affected by the Federal action.

Fern Bank Springs is included because recent research involving groundwater dye tracer tests indicates that Fern Bank Springs is hydrologically connected to the Edwards Aquifer (Johnson et al. 2012). However, there may be a groundwater divide between San Marcos Springs and Fern Bank Springs (Johnson et al. 2012). A groundwater divide indicates a degree of hydrological isolation. If there is no groundwater divide, drought and pumping in one segment of an aquifer may affect springflow in other parts of the aquifer. Additionally, Fern Bank Springs is located outside the jurisdiction of the EAA. In summary, we are uncertain about Fern Bank Springs relation to the Edwards Aquifer and include it in the action area to address the likelihood that Edwards Aquifer use may decrease Fern Bank Springs discharge and adversely affect the population of Comal Springs dryopid beetle associated with Fern Bank Springs.

Edwards and Trinity Aquifers and Selected Springs

The Edwards Aquifer consists of Cretaceous limestone and dolomite rocks of the Edwards Group and Georgetown Formation (Johnson et al. 2012, Musgrove and Crow 2012). The Edwards Aquifer south of the Colorado River is separated into two segments referred to as the Barton Springs and Southern segments. This consultation is focused primarily on the Southern Segment, which is sometimes referred to as the San Antonio Segment.

The Trinity Aquifer is closely related to the Edwards Aquifer. The Trinity Aquifer stretches across Texas in a narrow band from the Red River on the Oklahoma border through Hays County and south to Bandera and Medina counties. In Hays, Comal, Bexar and Medina counties, segments of the Edwards Aquifer overlay parts of the Trinity Aquifer. The Trinity Aquifer in these counties is thought to contribute thousands of acre-feet per year of groundwater to the Edwards Aquifer through faults and fissures (Mace et al. 2000, Jones et al. 2009, Jones 2011). While the extent of the inter-formational flow between these aquifers is not well understood, Jones (2011) estimated that the net groundwater flow from Trinity to the Edwards Aquifer ranged from 350 to 2,400 acre-feet per year per mile of aquifer boundary. The higher part of this range is associated with flow from Trinity to the Edwards Aquifer in Bexar and Comal counties.

The action area only includes a subset of the Southern Edwards Aquifer. The Southern Edwards Aquifer considered in this consultation extends from Kinney County east through Bexar County and then trends northeast to Hays County, bounded by a groundwater divide (Kyle Divide) in Hays County that tends to separate the Southern Edwards Aquifer from the Barton Segment of the Edwards Aquifer. The Southern Edwards Aquifer (south of the Kyle Divide) is about 160 miles long and varies from 5 to 40 miles in width. Water within the Edwards Aquifer displays complex and incompletely understood flow patterns, but generally flows from areas of higher elevation in the southwest to areas of lower elevation to the northeast. The Edwards Aquifer is the primary water source for municipal, industrial, agricultural, and domestic uses for more than two million people. The Edwards Aquifer in parts of Hays and Comal counties is habitat for

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Texas blind salamanders and Comal Springs invertebrates. The Edwards Aquifer is the source of springflows at Comal, San Marcos, and Hueco springs (Guyton and Associates 1979). Edwards Aquifer springflow is the primary determinant for habitat of the threatened and endangered species in this analysis.

The Edwards Aquifer is comprised of three zones referred to as the contributing (drainage), recharge, and artesian zones. Each of these zones displays unique hydrogeological characteristics. Precipitation falling across the contributing zone flows downstream to the recharge zone where it can enter the aquifer through recharge features (such as caves, sinkholes, faults, and fractures) or by infiltrating soils and rock strata that overlie the aquifer. Many creeks, streams, and rivers lose significant amounts and sometimes all of their baseflow to recharge features as they cross the recharge zone. The artesian zone is composed of less permeable geologic layers that confine the inflowing waters from the recharge zone. The hydraulic pressure of the confined water within the artesian zone’s cavities, faults, and fissures forces it to the surface where it escapes through numerous springs and seeps.

The Edwards Aquifer is the source of water for several major and minor springs, including Comal and Hueco springs in Comal County, and San Marcos Springs in Hays County. The Edwards Aquifer has a high capacity for rapid recharge, and rainfall over the contributing and recharge zones can quickly increase water levels within the aquifer. The Edwards Aquifer also experiences rapid drops in water levels due to pumping, especially during drought periods. For example, in 1990, Comal Springs flow dropped from 242 cfs on May 7 to 54 cfs on July 6 (USGS published data, USGS 08168710 Comal Springs at New Braunfels, TX). In this same period, the Bexar County Index Well, J-17 groundwater level dropped more than 32 ft. All of the species addressed in this biological and conference opinion depend on: (1) water discharged from the springs at Comal, San Marcos, and Hueco springs or (2) subterranean habitats within the Edwards Aquifer. The level of the Edwards Aquifer directly affects groundwater and discharge from these springs. A discussion of these springs progressing from south to north follows.

Comal Springs

Comal Springs is the largest spring group in Texas and the southwestern conterminous United States. Comal Springs and spring-fed Landa Lake support the largest known populations of the endangered Comal Springs invertebrates (See Figure 2). Designated critical habitat units for three of the species considered in this consultation (Comal Springs dryopid beetle, Comal Springs riffle beetle, and Peck’s cave amphipod) are located at the Comal Springs including parts of Landa Lake.

Recent spring mapping efforts in April 2012, by Texas Parks and Wildlife Department (TPWD) (Norris 2013) confirmed that the Comal Springs system consists of more than 300 springs (See Figure 3). Some of these springs are part of spring runs that flow into Landa Lake, an impoundment of the headwaters of the Comal River. The Comal River runs about 3.1 miles to its confluence with the Guadalupe River. The average discharge at Comal Springs for calendar years (CY) 1933 through 2011 was about 290 cfs.

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The severity of the 1949 to 1956 drought of record (DOR) and its impact on water levels at Landa Lake are unique in the hydrologic record for central Texas. The most critical period of low flow at Comal Springs was during the summer months of 1956, when Landa Lake dropped from average water surface levels in early June, to ceasing flow over the dam in August of that year. Spring runs No. 1 and No. 2 ceased flowing during the summer of 1953 and from the summer of 1954 until January 1957. Spring run No. 3 stopped flowing during the summer of 1955, and again from May until December in 1956. When the water elevation at the Landa Park well dropped to about 619 feet above msl, total spring discharge fell to zero. Spring discharge fell to zero for 144 consecutive days, from June 13 to November 3, 1956.

Hueco Springs

Hueco Springs is located in Comal County about three miles north of Comal Springs, and is the site of a designated critical habitat unit for one of the species considered in this consultation (Peck’s cave amphipod). This spring complex consists of two main groups of springs issuing from the floodplain of the Guadalupe River. Hueco I (main) is a large, typically perennial spring on the west side of River Road in an undeveloped area. This feature has reportedly stopped flowing during severe drought conditions including the drought of 1984 (Ogden et al. 1986). Hueco II (satellite) is an intermittent spring on the east side of River Road that typically stops flowing during the driest months each year (Puente 1976, Barr 1993, Guyton and Associates 1979). Springflow temperatures at Hueco Springs have been reported between 68 to 71°F (George 1952, Brune 1981).

San Marcos Springs

San Marcos Springs is the second largest spring system in Texas and has historically exhibited the greatest flow dependability and environmental stability of any spring system in the southwestern United States. Records indicate that the San Marcos Springs have never ceased flowing, although the discharge varies and is tied to fluctuations in the Edwards Aquifer.

The San Marcos Spring system today consists of multiple spring outlets along the shoreline and submerged beneath the surface of Spring Lake. Spring Lake was created when the spring-fed headwaters of the San Marcos River were impounded in 1849 by a dam constructed to operate a gristmill. The surface water and bottom of Spring Lake are owned by the State of Texas, and the State-affiliated Texas State University – San Marcos owns the surrounding lands.

Recent research based on hydrologic data, geochemistry, and groundwater tracer tests has shed light on the origin of flow at San Marcos Springs (Musgrove and Crow 2012, Johnson et al. 2012). San Marcos Springs receives regional contributions from the Edwards Aquifer artesian zone as well as local recharge (e.g., from the Blanco River).

The San Marcos River flows primarily southeastward for about 68 miles from its impounded headwaters at Spring Lake before joining the Guadalupe River near the city of Gonzales, in Gonzales County. From the upper part of Spring Lake downstream to the confluence with the Blanco River is about five miles in length (along the centerline of the waterway). The upper San Marcos River and Spring Lake are the sites of designated critical habitat units for five of the

Biological Opinion for JBSA Edwards Aquifer Use Page 7

species considered in this consultation (Texas wild-rice, Comal Springs riffle beetle, fountain darter, San Marcos gambusia, and the San Marcos salamander).

The rapidly flowing and primarily spring-fed San Marcos River is unusually clear in its uppermost reach and varies from about 16.4 to 49.2 feet in width and to about 13 feet deep. The river flows mostly over gravel or gravel/sand bottom with many shallow riffles alternating with deep pools. There is some variability in the substrate, and in areas with lower flows, silt and mud accumulates. Silt dominated substrates are common near eroded banks and stormwater drainage points. The upper San Marcos River is joined by four named and various unnamed creeks, various storm sewer outfalls, and the discharge from a wastewater treatment plant.

Springflows at San Marcos springs are directly related to water use from the Edwards Aquifer. The average discharge at San Marcos Springs for the period CY 1957 through 2011 was about 174 cfs. Much lower flows have occurred during drought conditions. Both the lowest recorded average monthly flow of 54 cfs recorded during 1956, and the lowest measured daily flow of 45.5 cfs on 15 and 16 August 1956 occurred during the DOR event (Guyton and Associates 1979).

Fern Bank Springs

Fern Bank Springs is located about eight miles northwest of San Marcos Springs on privately- owned land in a historically rural landscape. There are several springs collectively called Fern Bank Springs including springs providing flow to a cave and springs at lower elevations along the south bank of the Blanco River. Fern Bank Springs is the site of a designated critical habitat unit for one of the species considered in this consultation (Comal Springs dryopid beetle). Water temperatures at Fern Bank Springs have been reported as ranging between 68 to 71°F (George 1952, Brune 1981).

The spring system consists of a main outlet and a number of small springs that issue forth from a cliff overlooking the Blanco River. The exact water source for Fern Bank Springs is unknown, but may derive its flows from the Edwards Aquifer (Brune 1981, Johnson et al. 2012), the Glen Rose formation of the Trinity aquifer, or from the Blanco River (Veni in litt. 2006). Dye tracer test results suggest that some of the water at Fern Bank Springs may be sourced from areas south of Fern Bank Springs (Johnson et al. 2012). Fern Bank Springs discharges to the Blanco River just upstream of the Edwards Aquifer recharge zone and may provide some small contribution to Edwards Aquifer recharge. Johnson et al. (2012) indicated that under dry conditions the Blanco River may provide recharge for both San Marcos and Barton springs.

Fern Bank Springs discharge is not gaged and has only been intermittently measured. Brune (1981) reported Fern Bank spring flow discharge of 4.9 cfs on May 31, 1975, and 0.3 cfs on May 1, 1978. A single family owned the spring site from the late 1800s until 2009 and the landowner reported that the spring never ceased flowing during that time, including through the drought of the 1950s drought of record (DOR).

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Proposed Conservation Measures

Conservation measures are actions taken by the Federal agency to benefit listed or promote the recovery of listed species. JBSA has identified measures they will actively pursue to further reduce demand for water from the Edwards Aquifer and reduce pumping during times when water levels in the aquifer and spring flows are low. The JBSA has proposed to reduce its pumping as the water levels drop in the aquifer. Pumping is curtailed at five specific water level stages consistent with the current Edwards Aquifer Authority critical period management. The Wing Commander or his/her Designee in coordination with the Base Civil Engineer and all base organizations will authorize water restrictions throughout JBSA according to critical period stages shown in Table 1. A progressively more severe drought will trigger further pumping reductions.

Additional proposed water conservation efforts are summarized in sections 4.3 and 6.3 of the BA. JBSA will assess the feasibility and compatibility of various water conservation methods with its missions. These conservation measures include: (1) reducing water used for landscaping when possible, (2) installing low flow toilets and shower heads, (3) using recycled water whenever possible for non-potable purposes, and (4) water conservation education on and off- base. Using reclaimed wastewater effluent is one way to reduce Edwards Aquifer water withdrawal. The uses of non-potable reclaimed water are broad, with turf irrigation being the primary proposed use at the military facilities. Another water conservation objective is for employees to use water conservation measures at their off-base residences. This is done by educating employees on water conservation practices that could be implemented. Outreach programs also increase awareness of water conservation goals, practices, and achievements. Education and outreach could be in the form of kits, pamphlets, posters, ads, fact sheets, conservation training seminars, and incentive programs to reduce water use.

Further water conservation can come from improvements to infrastructure by studying and modifying the water distribution systems and water fixtures. These may include leak detection, repairs, metering, repair and replacement of faulty fixtures and conversion to low or no flow devices. Industrial conservation measures could include cooling tower water recycling studies, kitchen operations, car wash water recycling systems, and aircraft and large vehicle wash water recycling. Other miscellaneous conservation methods could include using pool covers, reusing water for irrigation, xeriscaping, rainwater and gray water collection, and curtailing use of ornamental fountains.

In addition to water conservation measures, the Service and JBSA have discussed means for the next 15 years to: (1) improve the status of threatened and endangered species adversely affected by Edwards Aquifer pumping, (2) actively seek partnerships and opportunities to support the regional habitat conservation efforts, and (3) funding EARIP efforts in a manner commensurate with JBSA’s proportion of overall Edwards Aquifer pumping.

The Service supports the principles guiding the Department of Defense’s Legacy program: stewardship, leadership, and partnership. JBSA has already shown its stewardship in water conservation. Consistent with the Act’s section 7(a)(1)(A) directive to use their authorities by carrying out programs for the conservation of threatened and endangered species, we encourage Biological Opinion for JBSA Edwards Aquifer Use Page 9

JBSA to continue to provide leadership by supporting Edwards aquifer conservation efforts. For example, on and near JBSA – Camp Bullis, JBSA is working to protect the Edwards Aquifer recharge water quality. Finally, strengthening JBSA partnerships with the Edwards Aquifer stakeholders will help ensure the success of the EARIP and our recovery efforts.

3. Status of the Species and Environmental Baseline

Species that may be affected by the action include the endangered Texas wild-rice, Comal Springs dryopid beetle, Comal Springs riffle beetle, Peck’s cave amphipod, fountain darter, San Marcos gambusia, San Marcos salamander, and Texas blind salamander.

The general distribution of species that may be affected is presented in Table 2. The best available information indicates that each of these localities is dependent at least in part on Edwards Aquifer levels.

The environmental baseline for all species considered in this document includes the EARIP HCP (2012). The EARIP HCP phase I continues through March 18, 2021; phase II starts no later than March 18, 2021 and continues for the balance of the 15-year HCP permit (March 31, 2028). One of the most important factors affecting the conservation of the subject species is the level of permitted well withdrawal from the Edwards Aquifer by non-Federal users. The EARIP HCP permit holders have made a commitment to maintain Comal and San Marcos springflows to ensure the species dependent on those springs survive in the wild. As the San Antonio region population grows, there will be increased water demands. One effect of this level of use is a greater reliance on critical period management to abate the decline in springflows. However, the permit holders have committed considerable resources to improve the resilience of threatened and endangered species in the wild as well as supporting expensive ex situ conservation.

3.a. Texas wild-rice

The entire range of Texas wild-rice (Zizania texana) is within the action area, and the status of this species therefore constitutes the environmental baseline for this species.

Species Description and Life History

Texas wild-rice was (TWR) listed as endangered on April 26, 1978 (43 FR 17910). TWR is an aquatic, monoecious (pistillate and staminate flowers are on the same plant), perennial grass, which is generally 1-2 m long and usually immersed in the flowing water of the San Marcos River. The inflorescence and the upper culms and leaves become emergent as flowering commences. Flowering and seed set occur primarily from late spring through fall but may occur sporadically at other times in warm years (Service 1996a). In slow moving waters, TWR plants function as annuals, exhibiting less robust vegetative growth, then flowering, setting seed, and dying within a single season.

San Marcos springflow is critical for growth and survival of TWR (Saunders et al. 2001). TWR relies on carbon dioxide as its inorganic carbon source for photosynthesis rather than the more commonly available bicarbonate used by most other aquatic plants (TPWD 1994, Power and

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Doyle 2004). Water from the Edwards Aquifer contains relatively high levels of dissolved carbon dioxide due to the calcium carbonate makeup of the region’s karstic geology and its nearly neutral pH. The upper San Marcos River is usually dominated by San Marcos springflows and TWR appears to grow best where dissolved free carbon dioxide is available as long as other habitat factors are supportive.

Reproduction of TWR occurs either asexually (clonally) through stolons or sexually via seeds. Asexual reproduction occurs where shoots arise as clones at the ends of rooting stolons (Emery and Guy 1979). Clonal reproduction appears to be the primary mechanism for expansion of established stands, but does not appear to be an efficient mechanism for dispersal and colonization of new areas. TWR segments have been observed floating downstream and some of these may become established plants if they become lodged in suitable substrate. Seed production may be essential for dispersal and establishment of new stands of TWR.

TWR inflorescences, upper culms, and leaves emerge above the water’s surface and wind- pollinated florets produce seed during sexual reproduction. This typically takes place in late spring through fall, though flowering and seed set may occur at other times in warm years (Service 1996). Triggers for flowering are not well understood. TWR seed is not long-lived, and viability begins to drop markedly within one year of production. No appreciable seed bank is thought to exist. In slow moving waters, TWR can function as an annual. Under these conditions, the species exhibits less robust vegetative growth, then flowers, sets seed, and dies within a single season.

TWR tillers have been observed floating downstream. Some of these tillers may become established plants if lodged in suitable substrate and appropriate physical habitat. Clonal reproduction appears to be the primary mechanism for expansion of an established stand, but it does not appear to be an efficient mechanism for dispersal and colonization of new areas. A life- history strategy using sexual reproduction for dispersal and asexual reproduction within the parental habitat is common in both plants and animals (Sebens and Thorne 1985). Seed production may be essential for dispersal and establishment of new stands in TWR.

Historic and Current Distribution

TWR occurs only in Spring Lake and the upper San Marcos River, above the confluence with the Blanco River. Plants form extensive stands in substrates of fine gravels, small gravels, sand, medium gravels, and silt (Saunders et al. 2001). Other native species that occur in the same general area of the river inhabited by TWR include pondweed (Potamogeton illinoensis), watercelery (Vallisneria sp.), arrowhead (Sagittaria platyphylla), hornwort (Ceratophyllum demersum), and water primrose (Ludwigia repens). Non-native species now commonly present include hydrilla (Hydrilla verticillata), East Indian hygrophila (Hygrophila polysperma), and Brazilian waterweed (Egeria densa).

When described in 1933, TWR was indicated to be abundant in the San Marcos River, including Spring Lake and its irrigation waterways (Silveus 1933, Terrell et al. 1978). In the 1960s and 1970s, investigators found very little TWR remaining. Estimated coverage of wild-rice in 1976 was 1,131 m2 (Emery 1977). BIO-WEST (2013) has provided the most recent estimate for TWR

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coverage. BIO-WEST reported total coverage from an August 3 – 10, 2012 wild-rice survey as 4,367.1 m2 . This represents an increase of about 19 percent from the BIO-WEST wild-rice survey (3,671.6 m2) in June 20 – 27, 2011 and BIO-WEST reported this was the most extensive coverage of wild-rice since they began annual surveys.

Several changes in the TWR coverage are noteworthy. A large flood occurred in October 1998 between the 1998 and 1999 surveys, which are typically conducted in July or August. TWR stands downstream of Interstate Highway 35 suffered significant losses. In August 2006, five wild-rice plants were lost in Segment E in the area between Rio Vista Dam and Cheatham Street Bridge. Researchers from BIO-WEST and TPWD noticed a significant loss of wild-rice in Segment A in 2006. It appears that sometime between August and late September of 2006, people destroyed about 237 m2 of the wild-rice in Segment A. As of August 2012, over 64 percent of TWR occurs in Segment B and about 88 percent of TWR occurs in Segments A, B, and C (i.e., upstream from the concrete pier Union Pacific - Katy railroad bridge, Rio Vista Park). Increased areal coverage range-wide is recommended for TWR recovery. TWR coverage may be increased by maintaining and enlarging existing wild-rice stands and through the establishment of new stands (naturally and artificially).

Reasons for Decline and Threats to Survival

Reduced springflow has been identified as the greatest threat to TWR (Service 1996a). Other threats include natural disasters such as droughts and floods, TWR habitat destruction and alteration, non-native species impacts, pollution, and unintended recreational impacts (Service 1996a, Poole et al. 2007).

Though TWR was described as abundant in 1933 (Silveus 1933), there are no other records of quantity or distribution of TWR before, during, or immediately after the multi-year drought of record (DOR), which ended in late 1956. The San Marcos River’s historic minimum monthly springflows of 54 cfs were recorded during the DOR in 1956. The next record of the species is the 1967 description that one plant remained in Spring Lake, and only scattered plants were found in the last 1.5 miles (2.4 km) of the upper San Marcos River (Emery 1967). This decline was attributed to several causes including dredging activities used to maintain the appearance of Spring Lake and the San Marcos River, plant collection, pollution, and the impact of floating debris that damaged the plant’s emergent inflorescences thus interfering with reproduction (Emery 1967). It is also likely that reduced springflow during the multi-year DOR event contributed to the decline and reduced range reported in 1967.

The species is intolerant of desiccation, and drought conditions that dewater portions of the river (as occurred in 1996) have reportedly killed exposed stands. Low flow events reduce river depth and bring wild-rice plants closer to the water’s surface. Under these conditions, floating mats of vegetation that normally move downriver can become lodged in stands of wild-rice. These mats shade the species and have reportedly interfered with flowering stem emergence, thereby impeding sexual reproduction and seed production believed important for species dispersal (Power 1996, 2002; Poole 2006).

The San Marcos River is located in one of the most flood-prone areas in the United States (Caran

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and Baker 1986). Though TWR evolved in a system exposed to occasional flooding events, scouring floods have been associated with decreasing populations of TWR. A flood event in 1998 is reported to have destroyed stands of the species in various segments of the river (Poole 2002, Edwards Aquifer Area Expert Science Subcommittee 2008).

Some research has suggested that altered substrate composition and modified current velocities associated with impoundments and urbanization effects have affected TWR biomass production and stem densities (Power 1996). Reductions in streamflow can impact the shallow-growing species by exposing plants to desiccation and increased herbivory by waterfowl and non-native species (Rose and Power 1992).

TWR is documented to be consumed by non-native species including nutria (Myocastor coypus) and giant ramshorn snails (Marisa cornuarietis). Introduced fishes such as suckermouth catfishes (Loricaridae) can disrupt substrates thereby increasing turbidity and may burrow into and destabilize riverbanks, thereby introducing additional sediment loads into the river system.

There are numerous non-native plant species in the San Marcos River system that can displace TWR through direct competition for space, light and nutrients. It has been suggested that these species may also alter the ecosystem in a manner that reduces habitat suitability for TWR. Such species include alligatorweed (Alternanthera philoxeroides), giant reed (Arundo donax), watersprite (Ceratopteris thalichtroides), elephant ear (Colocasia esculenta), Beckett’s water trumpet (Cryptocoryne beckettii), water-hyacinth (Eichornia crassipes), Brazilian waterweed (Egeria densa), hydrilla (Hydrilla verticillata), East Indian hygrophila (Hygrophila polysperma), water milfoil (Myriophyllum sp.), water lettuce (Pistia stratiotes), and watercress (Nasturtium officinale) (Bowles and Bowles 2001, Poole et al. 2007, Rosen 2000). Monitoring for water trumpet in the upper San Marcos River continues and it appears efforts to eliminate it there have largely been successful (P. Caccavale, San Marcos National Fish Hatchery and Technology Center, pers. comm, 2013).

TWR requires clean, flowing waters with adequate concentrations of dissolved carbon dioxide. Pollution such as groundwater contamination or as the result of a catastrophic event such as a hazardous material spill within the watershed or into the San Marcos River itself constitutes another threat to the species. The upper San Marcos River and its immediate tributaries are crossed by a total of 30 bridges, including three railroad bridges and six bridges associated with Interstate Highway 35. Any of these locations could be the source of a spill that could affect TWR. Stormwater inflows and other non-point sources of contamination may also pose a threat to the species.

Recreational use of the San Marcos River can also result in adverse impacts to TWR. Recreation in the San Marcos River has been reported as seasonal, with the highest use during summer months, holidays and weekends (Bradsby1994). A study that associated recreation activities with visible damage to TWR reported that tubing was associated with the greatest individual damage and dogs had the highest level of damage proportional to visits (Breslin 1997). These studies did not quantify effects to the species at various flow rates; though a greater percentage of the plants are presumably exposed to recreational activities when flow decreases, thereby increasing the potential for adverse impacts.

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This environmental baseline describes the current status of the species and is based upon impacts to which the species has been exposed (Service and NMFS 1998). To understand the potential effects of the aquifer management under the EARIP HCP, springflow was modeled for a 54-year period (1947 through 2000), which includes the DOR (1949 to 1956). With full implementation of the EARIP HCP, San Marcos Springs flow is projected to remain above 51 cfs (monthly mean) even during a repeat of the conditions similar to the DOR. In addition, to maintain San Marcos springflow above 51 cfs, the EARIP HCP is planning and implementing local conservation efforts to reduce anthropogenic stressors to TWR stands.

Survival Needs and Recovery Criteria

The San Marcos and Comal Springs and Associated Aquatic Ecosystems Recovery Plan (Service 1996a) identified several recovery criteria for TWR, including:

i. Ensuring adequate flows and water quality in Spring Lake and the San Marcos River; ii. Maintenance of genetically diverse reproductive populations in captivity; iii. Creation of reintroduction techniques for use in the event of a catastrophic event; iv. Removal or reduction of local threats from non-native species, recreational users, and habitat alteration; and, v. Maintenance of healthy, self-sustaining, reproductive populations in the wild.

Factors affecting the Species within the Action Area

TWR has been the subject of eight formal consultations for Federal actions unrelated to the action considered here. The Service consulted on two stormwater outfalls and the replacement of two bridges that impacted the San Marcos River. The USACE consulted with the Service on repairs to the main spillway of Spring Lake Dam and an aquatic restoration project at Spring Lake. The Service completed an intra-Service consultation regarding the pumping of Edwards Aquifer water that supports the continuing operations and refugia of the San Marcos National Fish Hatchery and Technology Center and the Uvalde National Fish Hatchery. Lastly, the Service completed an intra-Service consultation (January, 2013) regarding the issuance of incidental take permit (March 18, 2013) for Edwards dependent species to the EARIP and their regional management plan (HCP) for the Edwards Aquifer. None of these consultations determined that the considered actions would jeopardize TWR or result in destruction or adverse modification of designated critical habitat.

On December 17, 1982, the Texas Parks and Wildlife Commission placed Texas wild-rice on the State endangered list (Texas Register 1982). Section 88.001 of the Texas Parks and Wildlife Code and §65.171 of the Texas Administrative Code (TAC) prohibit take of an endangered plant for commercial sale from private or public land, except under a State Scientific Research or Non- game Collection Permit. ‘‘Take’’ of an endangered plant is defined in § 88.001 of the TPW Code as to collect, pick, cut, dig up, or remove. There are no provisions under the Texas Threatened and Endangered Species Regulations for reducing or eliminating the threats that may adversely affect TWR or its habitat.

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The TPWD is authorized to establish State Scientific Areas for the purposes of education, scientific research, and preservation of flora and fauna of scientific or educational value. To promote conservation of listed species and minimize the impacts of recreational activities on such species and their habitats, TPWD designated a State Scientific Area encompassing a two mile segment of the San Marcos River effective May 1, 2012.

This designation authorizes the TPWD to limit recreation within designated areas when San Marcos River flows fall below 120 cfs. The designation provides for continued recreational use of the waterway by maintaining open channels outside of protection zones that run the length of the river. These areas allow for continued use of the river even during low flow periods for activities such as tubing, canoeing, kayaking, and swimming.

The regulation makes it unlawful to move, deface, or alter any signage, buoys, booms, or markers delineating the boundaries of the State Scientific Area; to uproot TWR within the area; or to enter any such marked areas. The City of San Marcos and Texas State University have committed to install kiosks at key locations identifying access points, exclusion areas, and to provide educational information about the State Scientific Area and the species and their habitats it is intended to conserve.

Because the designated State Scientific Area in the San Marcos River has only recently been established, no information has yet been collected concerning the Area’s effect on listed species including TWR.

Critical Habitat

Texas wild-rice critical habitat was designated on July 14, 1980, and is described as Spring Lake and the San Marcos River downstream to its confluence with the Blanco River (45 FR 47355). All designated critical habitat for TWR is contained within the action area considered in this consultation.

The designation of critical habitat for TWR predates the October 1, 1984, regulation (49 FR 38900) stipulating that primary constituent elements (PCE) essential for the conservation of the species be identified at the time critical habitat is designated. However, in the final published rule (45 FR 47355) the Service describes actions that would adversely modify designated critical habitat, including those that would significantly alter the flow or water quality in the San Marcos River; physically alter Spring Lake or the San Marcos River, such as dredging, bulldozing, or bottom plowing; or physically disturb the plants, such as harrowing, cutting, or intensive collecting. Based on the final rule, the primary constituent elements could generally be defined as:

TWR PCE 1. Clear water, TWR PCE 2. Natural springflow regime, TWR PCE 3. Constant year-round temperature, and TWR PCE 4. Maintenance of the natural substrate free from anthropogenic disturbance.

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Clear water is currently available in the designated critical habitat for TWR under most conditions. Activities that contribute sediment loads, such as non-point source erosion from the urbanizing areas surrounding the upper San Marcos River, or activities that suspend existing sediments such as lake-bottom disturbances by SCUBA divers in Spring Lake or swimmers in the San Marcos River, can increase turbidity and impact this element. Such turbidity in Spring Lake and the San Marcos River usually dissipate as the suspended particulates flow downstream or settle out of the water column in relation to flow rate. Continual or repeated re-suspension of particulates can markedly reduce water clarity. This can be observed downstream of popular recreation sites in the river during periods of intense use, such as weekends, holidays, and May through September.

The San Marcos Springs flow regime is the result of precipitation and recharge that contribute to aquifer levels as they are affected by pumping throughout the region. Current aquifer management regulations limit pumping during drought conditions by specified amounts triggered primarily by the Bexar and Uvalde index well levels and Comal Springs, and to a lesser extent San Marcos springflow. These mechanisms have maintained continual springflows since they were enacted, though drought conditions during this time period have not approached the severity and duration of the DOR.

Temperature at San Marcos Springs reportedly varies less than 0.9°F near the headwater springs (Guyton and Associates 1979). Slattery and Fahlquist (1997) reported San Marcos River water temperature at the current river gauging station (University Drive Bridge)(July – August 1994) had a range of 4°F. Vaughan (1986) reported a constant springflow temperature of 70.7°F, with temperature ranges of 68.7°F in February to 77.9°F in August at the most downstream extent of occupied TWR habitat in the San Marcos River.

Substrates within the designated critical habitat for TWR have been affected by sedimentation related primarily to urbanization effects within the upper San Marcos River watershed. Sediment bars have been created within the river channel just downstream of Spring Lake dam and within the river segment that runs through Sewell Park as a result of these impacts. Substrates in portions of the designated critical habitat maintain a more natural character.

Adverse impacts from water recreationists, vandalism, floating vegetation mats, substrate disturbance, shading, herbicides in runoff, depredation by waterfowl and invertebrates, and suboptimal (or unsuitable) water depths and velocities are all factors affecting TWR critical habitat.

3.b. Peck’s cave amphipod

The entire range of the Peck’s cave amphipod (Stygobromus pecki) is within the action area, and this species description constitutes the environmental baseline for this species.

Species Description and Life History

Peck’s cave amphipod is a subterranean-adapted aquatic crustacean first collected in 1964 at

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Comal Springs. The species is eyeless and unpigmented (Holsinger 1967). Verification of this species is usually not possible in the field, as microscopic examination of adult specimens is usually required. Peck’s cave amphipod was listed as endangered on December 18, 1997 (62 FR 66295).

Some evidence suggests Peck’s cave amphipod is omnivorous, and can feed as a predator, scavenger or detritivore (Service 2007). Food sources may include living materials, detritus, leaf litter, and decaying roots. The species may also feed on bacteria and fungi associated with decaying plant material.

Peck’s cave amphipod inhabits the subterranean spaces associated with springs issuing from the Edwards Aquifer. The species has been reported from gravel, rocks, and organic debris (leaves, roots, wood) immediately inside of or adjacent to springs, seeps and upwellings of Comal Springs and Landa Lake (Gibson et al. 2008). Collections of the species from Panther Canyon well support early characterizations of the species as being associated at least in part with deep groundwater habitats (Holsinger 1967).

Little is known about Peck’s cave amphipod reproduction and life span in the wild. Mature and immature life stages have been collected near spring outlets, from seeps along the spring runs, and from Panther Canyon Well (Gibson et al. 2008). Limited and intermittent reproduction has occurred with captive stock in aquaria at the San Marcos Aquatic Resource Center (formerly known as the San Marcos National Fish Hatchery and Technology Center). Other troglobitic species of amphipods are known to live for as many as 5 to 6 years in stable habitats with relatively continuous inputs of food materials (Culver 1982).

Genetic analyses using mitochondrial DNA of known Peck’s cave amphipod populations were made by Nice and Ethridge (2011). They found two distinct haplotype groups without an apparent geographic structure with respect to the groups. A haplotype is defined by Allendorf and Luikart (2007) as “a combination of alleles at loci that are found on a single chromosome or DNA molecule.” One hypothesis is the presence of two cryptic species (in the Comal Springs - Edwards Aquifer system) within the nominal species Stygobromus pecki. However, more genetic analyses (including nuclear DNA) are needed to test this hypothesis. A formal peer- reviewed taxonomic description revising this species has not been published.

Historic and Current Distribution

Peck’s cave amphipod has been collected from Comal Springs, Hueco Springs, and in Panther Canyon well. Panther Canyon well is about 360 feet (110 m) from Comal Springs Spring run No. 2 (Holsinger 1967, Arsuffi 1993, Barr 1993, Gibson et al. 2008). Panther Canyon well is a monitoring well consisting of a cased borehole about 6 inches in diameter situated inside of a small well house. Dye tracing efforts led by EAA have demonstrated connectivity between Panther Canyon Well and Comal Spring run No. 3 (LBG-Guyton and Associates 2004).

Researchers examining amphipod assemblages from springs, caves, and wells in Comal, and neighboring Hays and Bexar counties have yet to confirm the presence of the species from any other locations (Holsinger 1967, 1978; Holsinger and Longley 1980; Barr 1993; Gibson et al.

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2008). This suggests that Peck’s cave amphipod may be confined to groundwater conduits in the vicinity of spring openings as opposed to generally inhabiting the aquifer at large.

The Peck’s cave amphipod’s specialized subterranean and aquatic adaptations indicate that the species evolved in subterranean areas within the aquifer. However, the vast majority of the Peck’s cave amphipods collected to date have been found near spring openings of Comal Springs and Hueco Springs, and nearby spring run habitat. Figure 2 shows the areas in the Comal Springs system where surveys have found Peck’s cave amphipods and other Comal Springs invertebrates. Table 3 provides the size of these areas, the estimated density of Peck’s cave amphipod in spring-dominated habitat, and local population size estimates. Based on the best available scientific and commercial information, we estimate a total surface population of at 21,700 based on sampling and collection data (Bowles and Sanford unpublished field data, 1994; Bowles et al. 2003; Gibson et al. 2008)(see Figure 2 and Table 3). The last time a Peck’s cave amphipod was collected at Hueco Springs was August 16, 2003. The Peck’s cave amphipod abundance at Hueco Springs is unknown and has not been adequately characterized. However, the continued presence of this species at Hueco Springs, which ceases to flow during drought conditions, would support the hypothesis that this species may, on occasion, be able to recolonize spring habitats from subterranean aquatic habitats.

Reasons for Decline and Threats to Survival

At the time the species was listed, the Service identified reduction or loss of water of adequate quality and quantity as the main threats to the Peck’s cave amphipod, and that this decline is due primarily to human activities including withdrawal of water from the Edwards Aquifer (62 FR 66295).

To estimate the effect of the EARIP HCP management, springflow at Comal Springs was modeled for a 54-year period (1947 through 2000) that included the low recharge conditions of the DOR (1949 to 1956). With full implementation of the bottom-up program of the EARIP HCP, total Comal Springs flow is projected to remain above 27 cfs (monthly mean) even during a repeat of the DOR. However, if this situation occurs, springflow in Comal Springs spring runs No. 1 and 2 would be expected to fail. Should DOR conditions reoccur, surface habitats used by Peck’s cave amphipods will be reduced and areas associated with higher elevation springs that are currently suitable will be dewatered and become unsuitable.

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The environmental baseline describing the current status of the species is based upon impacts to which the species has been exposed (Service and NMFS 1998). During the DOR in 1956, Comal Springs ceased flowing for four months. However, we have no information on the fate of Peck’s cave amphipod populations in that period.

Survival Needs and Recovery Criteria

The chief survival need identified in the Peck’s cave amphipod listing rule is conservation of suitable habitat to sustain populations of the species. The conservation of Peck’s cave amphipod habitat includes maintenance of water quality and continuous natural springflow. No Recovery Plan has been finalized for the Peck’s cave amphipod at this time, though a Recovery Team has been convened and a Recovery Plan that will include Recovery Criteria is currently being drafted.

Factors affecting the Species within the Action Area

Peck’s cave amphipod has been the subject of four formal consultations for Federal actions unrelated to the action considered here. The USACE has consulted twice with the Service for bank stabilization and structural repairs to a bridge over Comal Springs. The Service completed an intra-Service consultation regarding the pumping of Edwards Aquifer water that supports the continuing operations and refugia of the San Marcos National Fish Hatchery and Technology Center and the Uvalde National Fish Hatchery. The Service completed an intra-Service consultation (January, 2013) regarding the issuance of incidental take permit (March 18, 2013) for Edwards dependent species to the EARIP and their regional management plan for the Edwards Aquifer.

The incidental take of 683 Peck’s cave amphipods has been authorized under these consultations. None of these consultations resulted in a determination that the considered actions would jeopardize the Peck’s cave amphipod or result in destruction or adverse modification of designated critical habitat.

On January 8, 2010, the Texas Parks and Wildlife Commission placed Peck’s cave amphipod on the State list of endangered species (Texas Register 2010). Section 68.002 of the TPW Code and § 65.171 of the TAC prohibit take of a threatened species, except under a State Scientific Research or Non-game Collection Permit. ‘‘Take’’ is defined in §1.101(5) of the TPW Code as to collect, hook, hunt, net, shoot, or snare, by any means or device, and includes an attempt to take or to pursue in order to take. There are no provisions under the Texas Threatened and Endangered Species Regulations for reducing or eliminating the threats that may adversely affect Peck’s cave amphipod or its habitat.

Critical Habitat

Critical habitat for Peck’s cave amphipod was designated on July 17, 2007 in two locations referred to as the Comal Springs and Hueco Springs Units (72 FR 39248), both of which are wholly within the action area described for this consultation.

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Designated critical habitat for the Peck’s cave amphipod in the Comal Springs Unit is described as aquatic habitat within Landa Lake and outlying spring runs that occurs from the confluence of Blieders Creek at the upstream end of Landa Lake down to the lake’s lowermost point of confluence with Spring run No. 1, and land along the shoreline of Landa Lake and islands within a 50-ft distance from spring outlets. Critical habitat does not include other areas of the lake bottom in areas where springs are absent (72 FR 39248).

In the Hueco Springs Unit, critical habitat was designated as the aquatic habitat and land areas within 50-ft from habitat spring outlets, including the main outlet of Hueco Springs and its associated satellite springs. The critical habitat designated for the Peck’s cave amphipod includes only aquatic habitat and land areas where PCE exist for this species. Areas consisting of buildings, roads, sidewalks, campgrounds, and lawns are excluded (72 FR 39248).

Primary threats to designated critical habitat may vary for individual springs according to the degree of urbanization and availability of aquifer source water, but possible threats generally include prolonged cessation of spring flows as a result of the loss of hydrological connectivity within the aquifer (e.g., groundwater pumping, excavation, concrete filling), pollutants (e.g., stormwater drainage, pesticide use), and non-native species (e.g., biological control, sport fish stocking). Management actions may be required to address these threats, such as maintaining a sustainable amount of groundwater, using of adequate buffers for water quality protection, selecting appropriate pesticides, and implementing integrated pest management plans (72 FR 39248).

The primary constituent elements (PCE) identified in the Critical Habitat designation for the Peck’s cave amphipod (PCA) include:

PCA PCE 1. High-quality water with no or minimal levels of pollutants, such as soaps and detergents and other compounds containing surfactants, heavy metals, pesticides, fertilizer nutrients, petroleum hydrocarbons, pharmaceuticals and veterinary medicines, and semi-volatile compounds, such as industrial cleaning agents, and including: (a) Low salinity with total dissolved solids that generally range from 307 to 368 mg/L; and (b) Low turbidity that generally is less than 5 nephelometric turbidity units; PCA PCE 2. Aquifer water temperatures that range from approximately 68 to 75°F (20 to 24°C); and, PCA PCE 3. Food supply that includes detritus (decomposed materials), leaf litter, living plant material, algae, fungi, bacteria and other microorganisms, and decaying roots.

The Comal Springs designated critical habitat unit currently provides each of the primary constituents identified in the rulemaking. Water quality within Landa Lake and the identified spring runs remains free of contaminants, and salinities and turbidity have not been reported to exceed the identified requirements. Comal Springs temperatures reportedly remain nearly constant (annual reported mean 74.1°F), and food supplies described in the critical habitat designation are present.

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Hueco Springs and its associated critical habitat unit consists of a large spring on the west side of that has reportedly stops flowing during severe drought events (Ogden et al. 1986), and an intermittent spring on the east side of River Road that typically stops flowing during the driest months each year (Puente 1976, Barr 1993, Guyton and Associates 1979). These springs are both located on private property, and researchers have had only limited and irregular access to this site. Information about the designated critical habitat and the ability of the crucial habitat unit to continue to provide primary constituent elements essential for the conservation of the species is therefore limited.

The Service proposed a revision to PCA critical habitat on October 19, 2012. The PCE of the proposed critical habitat is nearly identical to the designated PCA PCE except the first PCE includes the following: “hydrologic regimes similar to the historical pattern on the specific sites, with continuous surface flow for the spring sites and in the subterranean aquifer”. The proposed critical habitat units for Comal Springs and Hueco Springs include a critical habitat subsurface area that extends 360 feet horizontally from the Critical Habitat Surface area. The proposed revisions to PCA critical habitat are discussed further in Section 8 of the biological opinion.

3.c. Comal Springs dryopid beetle

The entire range of the Comal Springs dryopid beetle (Stygoparnus comalensis) is within the action area, and this status of the species therefore constitutes the environmental baseline for this species. Species Description and Life History

The Comal Springs dryopid beetle (CSDB) was listed as endangered on December 18, 1997 (62 FR 66295). The only known hypogean-adapted (subterranean) member of the family Dryopidae, the species was described based on its unique morphological distinctions including vestigial (poorly developed and non-functioning) eyes and wings (Barr and Spangler 1992).

Larvae are elongate, cylindrical, yellowish brown, and reach about 0.24 to 0.31 inches (6.0 to 7.8 millimeters [mm]) in length (Barr and Spangler 1992). Larvae in the family Dryopidae do not have gills and are considered terrestrial, inhabiting moist soil along stream banks (Brown 1987, Ulrich 1986). The presence of vestigial eyes indicates adaptation to subterranean habitats. Larval development is unknown and pupae for this species have not been described. Bowles and Stanford’s surveys (July 1993 – April 1994) found 164 Comal Springs dryopid beetles in their samples of Comal Spring runs No. 1 through 4. Of these, larva (n=120) accounted for about 73 percent of CSDB found.

Adult Comal Springs dryopid beetles are elongate, parallel-sided and slender, with retractile head and translucent reddish-brown cuticle (Barr and Spangler 1992). Habitat for the Comal Springs dryopid beetle has been described as the soil, roots, and debris exposed above the waterline on the ceilings of spring orifices (Barr and Spangler 1992). Though restricted to aquatic environments by their reliance on a plastron for respiration (a gas film produced by an area of dense water-repelling hairs), adult Comal Springs dryopid beetles cannot swim (Brown 1987, Resh et al. 2008). Adult beetles crawl at a relatively slow pace.

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Dryopid adults typically feed on biofilm (microorganisms and debris) scraped from surfaces such as rocks, wood, and vegetation (Brown 1987). Potential food sources may include detritus (decomposed materials), leaf litter, and decaying roots. However, it is possible that this species may feed on bacteria and fungi associated with decaying plant material (J.R. Gibson, Service, pers. comm. 2006). A few wild caught adult specimens have survived in captivity 11 to 21 months (Barr and Spangler 1992, Fries et al. 2004), but lifespan is unknown.

Historic and Current Distribution

Comal Springs dryopid beetles were first collected in 1987 from the headwaters and springs along both banks of Comal Springs Spring run No. 2 (Barr and Spangler 1992). The species has subsequently been documented at Comal Spring runs No. 1 through No. 5; in seeps along the western shoreline of Landa Lake; in upwellings within Landa Lake near Spring Island, and in Panther Canyon Well (about 360 feet from the head of Comal Springs Spring run No. 2) (BIO WEST 2003-2009; Bowles et al. 2003; Fries et al. 2004; Gibson et al. 2008; Gibson, pers. comm., 2012). The species has also been documented at Fern Bank Springs, located about 19.6 miles northeast of Comal Springs in Hays County (Barr 1993, Gibson et al. 2008). The extent of the subterranean range of the species is unknown, though it has been suggested that they may be confined to small areas surrounding spring openings (Barr 1993, 62 FR 66295).

The Comal Springs dryopid beetle’s specialized subterranean and aquatic adaptations indicate that the species evolved in and occupies subterranean areas within the aquifer. Comal Springs dryopid beetles rely primarily on these subterranean habitats near springs and wetted areas near the spring openings. Based on the best available scientific and commercial information, we estimate a total surface population of Comal springs dryopid beetles in the Comal Springs system at 1,839 individuals (Bowles and Stanford, unpublished field data 1994; Bowles et al. 2003, Gibson 2011) with the most of these occurring in Comal Spring run No. 1. (see Figure 2 and Table 3).

Reasons for Decline and Threats to Survival

The listing rule describes reduction or loss of water of adequate quality and quantity as the main threat to the Comal Springs dryopid beetle, and States that this decline is due primarily to human activities including withdrawal of water from the San Antonio segment of the Edwards Aquifer (62 FR 66295). Comal Springs dryopid beetle larvae are found in moist soils and adults are restricted to aquatic environments by their reliance on a plastron for respiration. Loss of streamside soil moisture may therefore affect larvae, and the aquatic habitats occupied by adults are likely to be lost through drying or decreased spring flows during drought conditions.

The Comal Springs dryopid beetle is only known from two locations, and the non-swimming flightless aquatic beetle has limited opportunities to expand its range. The species is therefore presumed to have survived the DOR at Comal Springs and Fern Bank Springs, though because the species first collected in 1987 there are no records of species abundance and distribution before, during, or immediately after the DOR event, when Comal Springs stopped flowing for four-months.

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Contamination from a variety of sources including, but not limited to, human waste (particularly from septic tanks), agricultural chemicals, urban runoff, and transportation of hydrocarbons and other potentially harmful materials throughout the Edwards Aquifer recharge zone and watershed have been identified as threats to water quality (62 FR 66295). The fine hydrophobic hairs on the abdomen of adults of the species can lose their capacity to trap the thin film of air through which these beetles respire when exposed to surfactants or solvents such as those found in soaps and detergents. Pollution such as groundwater contamination or as the result of a catastrophic event such as a hazardous material spill or other release within the watershed or into Landa Lake or its immediate tributaries constitutes another threat to the species. Landa Lake and its immediate tributaries are crossed by a total of five bridges, any of which could be the source of a spill that could affect the species or its designated critical habitat unit at Comal Springs. Stormwater inflows and other non-point sources of contamination may also pose a threat to the species.

Modeling the same 54-year period using actual pumping totals rather than the maximum amount of pumping permitted provides a projection that may more accurately reflect current water use, including increased efficiency of agricultural operations and increased water conservation efforts throughout the region. Modeled Comal springflows using EARIP management indicates total Comal Springs discharge (monthly mean) would be less than 96 cfs during a repeat of DOR recharge conditions (EARIP HCP Phase I and II Springflow Modeling, HDR Engineering, Inc. et al. 2011). Based on research provided by Paul Thornhill (1993), total Comal Springflow in this range means Comal Springs Spring run No. 1 would cease flowing for 36 months. LBG – Guyton and Associates (2004) reported elevations for spring orifices in Spring runs No. 1 and 2. Spring run No. 1 openings (orifices) at the head of the spring run varied from 624.2 to 622.1 ft. Spring run No. 2 is fed by multiple orifices but LBG – Guyton reported only one (opening elevation: 622.6 ft). As the Edwards Aquifer levels decline, spring flow is controlled by these spring orifice elevations. While CSDB have been found in Landa Lake, the vast majority of CSDB collected have been from Comal Spring run No. 1 and 2. The reduction and loss of springflows during severe drought conditions projected by these modeling efforts could have significant impacts to the epigean (surface) populations of the Comal Springs dryopid beetle.

Survival Needs and Recovery Criteria

The chief survival need of the Comal Springs dryopid beetle identified in the listing rule is conservation of suitable habitat to sustain populations of the species. The conservation of Comal Springs dryopid beetle habitat includes maintenance of water quality and continuous natural springflow. No recovery plan has been finalized for the Comal Springs dryopid beetle, and no recovery criteria have been crafted for this species. A recovery team has been convened to

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address the needs of this species and a recovery plan that will include recovery criteria is currently being drafted.

Factors affecting the Species within the Action Area

The Comal Springs dryopid beetle has been the subject of four formal consultations unrelated to the subject action. The unrelated formal consultations include two USACE consultations for a bank stabilization and bridge repair. The Service completed an intra-Service consultation regarding the pumping of Edwards Aquifer water that supports the continuing operations and refugia of the San Marcos National Fish Hatchery and Technology Center and the Uvalde National Fish Hatchery. The incidental take of 93 Comal Springs dryopid beetles has been authorized under these non-HCP consultations. None of these consultations resulted in a determination that the considered actions would jeopardize the Comal Springs dryopid beetle or result in destruction or adverse modification of designated critical habitat. Recently, the Service completed an intra-Service consultation (January, 2013) regarding the issuance of incidental take permit (March 18, 2013) for Edwards dependent species to the EARIP and their regional management plan for the Edwards Aquifer. The EARIP received incidental take authorization for no more than 1,543 Comal Springs dryopid beetles.

On April 27, 2012, the Texas Parks and Wildlife Commission amended the State List of Endangered Species (31 TAC §65.176) to include the Comal Springs dryopid beetle (Texas Register 2012). Section 68.002 of the TPW Code and § 65.171 of the TAC prohibit take of endangered species, except under a State Scientific Research or Non-game Collection Permit. ‘‘Take’’ is defined in § 1.101(5) of the TPW Code as collect, hook, hunt, net, shoot, or snare, by any means or device, and includes an attempt to take or to pursue in order to take. There are no provisions under the Texas Threatened and Endangered Species Regulations for reducing or eliminating the threats that may adversely affect the Comal Springs dryopid beetle or its habitat.

Critical Habitat

Comal Springs dryopid beetle critical habitat was designated on July 17, 2007 in two units, referred to as the Comal Springs Unit and the Fern Bank Springs Unit (72 FR 39248). Both of these designated critical habitat units are within the action area considered in this consultation.

The Comal Springs Unit includes aquatic habitat within Landa Lake and outlying spring runs that occur from the confluence of Blieders Creek at the upstream end of Landa Lake to the lake’s lowermost point of confluence with Spring run No. 1; and land along the shoreline of Landa Lake and small islands within a 50-ft distance of spring outlets. Critical habitat in the Fern Bank Springs Unit includes aquatic habitat and land areas within a 50-ft distance from spring outlets, including the main outlet of Fern Bank Springs and its associated seep springs.

These designated critical habitat units include only aquatic and shoreline areas where primary constituent elements exist and do not include areas where these features do not occur, such as lawns, buildings, roads, parking lots, and sidewalks. Where lakes are included, critical habitat is only designated within a 50-ft radius around springs and does not include other areas of the lake bottom in areas where springs are absent.

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Primary threats to designated critical habitat may vary for individual springs according to the degree of urbanization and availability of aquifer source water, but possible threats generally include prolonged cessation of spring flows as a result of the loss of hydrological connectivity within the aquifer (e.g., groundwater pumping, excavation, concrete filling), pollutants (e.g., stormwater drainage, pesticide use), and non-native species (e.g., biological control, sport fish stocking). To address these threats management actions may be required. Examples of management actions include maintenance of sustainable groundwater use and subsurface flows, use of adequate buffers for water quality protection, selection of appropriate pesticides, and implementation of integrated pest management plans (72 FR 39248).

The primary constituent elements identified in the Critical Habitat designation for the Comal Springs dryopid beetle are:

CSDB PCE 1. High-quality water with no or minimal levels of pollutants, such as soaps and detergents and other compounds containing surfactants, heavy metals, pesticides, fertilizer nutrients, petroleum hydrocarbons, pharmaceuticals and veterinary medicines, and semi-volatile compounds, such as industrial cleaning agents, and including: (a) Low salinity with total dissolved solids that generally range from 307 to 368 mg/L; and, (b) Low turbidity that generally is less than 5 nephelometric turbidity units;

CSDB PCE 2. Aquifer water temperatures that range from approximately 68 to 75°F (20 to 23.9°C);

CSDB PCE 3. A hydrologic regime that allows for adequate spring flows that provide levels of dissolved oxygen in the approximate range of 4.0 to 10.0 mg/L for respiration of the Comal Springs dryopid beetle; and,

CSDB PCE 4. Food supply that includes detritus (decomposed materials), leaf litter, living plant material, algae, fungi, bacteria and other microorganisms, and decaying roots.

The Comal Springs designated critical habitat unit currently provides each of the primary constituents identified in the rulemaking. Water quality within Landa Lake and the identified spring runs remains free of contaminants, and salinities and turbidity have not been reported to exceed the identified requirements. Comal Springs temperatures reportedly remain nearly constant (annual reported mean 74.1°F), and springflows continue to maintain dissolved oxygen levels supportive of the species. Food supplies as described in the critical habitat designation are present.

Fern Bank Springs and its associated critical habitat unit are both wholly located on private property, and researchers have had only limited and irregular access to this site. Information about the designated critical habitat and the ability of the crucial habitat unit to continue to

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provide primary constituent elements essential for the conservation of the species is therefore limited. The discharge at Fern Bank Springs has only been intermittently measured. Brune (1981) reported Fern Bank spring flow discharge of 4.9 cfs on May 31, 1975, and 0.3 cfs on May 1, 1978. A single-family owned the spring site from the late 1800s until 2009, and in 2008, the landowner reported that the spring never ceased flowing during that time, including through the drought of the 1950s. There are, however, no data to either support or refute this claim.

At the time of this writing, a proposed rule to revise critical habitat for the Comal Springs dryopid beetle has been published in the Federal Register in accordance with the settlement agreement, and public review and comment have been solicited. Because no change in designation has been established through rule-making, this analysis relies on the critical habitat designation currently in place. An analysis of the proposed revision of the designated critical habitat is found in the Conference Opinion (Section 8) that follows.

3.d. Comal Springs riffle beetle

The entire range of the Comal Springs riffle beetle (Heterelmis comalensis) is within the action area, and this status of the species therefore constitutes the environmental baseline for this species.

Species Description and Life History

The Comal Springs riffle beetle (CSRB) is a small aquatic beetle first described in 1988 (Bosse et al. 1988). The species was listed as endangered on December 18, 1997 (62 FR 66295).

Larval Comal Springs riffle beetles are elongate, tube-shaped, and light tan. The CSRB pupa is pale and legs and wing pads project loosely from the body. The number of larval instars among species in the family Elmidae ranges from 5 to 8 (Brown 1987), but the specific number of instars for CSRB is unknown. The incubation period of elmid eggs typically ranges from 5 to 15 days, and the larval stages may last from 3 to 36-months (Brown 1987) before pupation occurs. Brown (1987) noted that mature elmid larvae pupate in protected areas above the water line.

Adult CSRBs are reddish brown, and range in length from 0.067 to 0.83 inches (1.7 to 21.0 mm). The sides of the body are approximately parallel and the entire dorsal surface is coated with fine golden-colored setae (hairs) (Bosse et al. 1988). The hind wings of CSRBs are short and non functional and the species is incapable of flying (Bosse et al. 1988).

Larval and adult CSRB populations at Comal Springs may reach their greatest densities (about 5 per square meter) in late fall through winter, but all life stages can be found throughout the year suggesting multiple broods in a season with overlapping generations (Bowles et al. 2003). Completion of the life cycle in CSRBs from egg, to larvae, to adult has been reported as requiring six-months to three-years (BIO-WEST 2006). Density of CSRB (larva and adults combined) ranged from 2.9 to 3.7 individuals per square meter in Comal Spring runs No. 1, 2, and 3 (Bowles and Stanford 1994). Reproduction in captivity has been sporadic (Fries 2003).

The CSRB is an epigean (surface-dwelling) species that inhabits fast flowing waters with gravel

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and cobble substrates (Bowles et al. 2003). Food sources include, but are not limited to, detritus, leaf litter, and decaying roots. Little is known of their life history and habitat (Bowles et al. 2003).

Recent research describes the species’ strong associations with springs, and microhabitat preferences for spring outlet conditions and water quality parameters characteristic of Edwards Aquifer spring water. In experiments, the CSRB exhibited preferences for temperatures near 73.4°F, elevated free carbon dioxide , darkness, and a lower range of water velocities (Cooke 2012). Nice and Gonzales (2007) and Gonzales (2008) described the genetic structure of the Comal Springs surface population of CSRB.

Historic and Current Distribution

The CSRB was first collected at Comal Springs in 1976 (Bosse et al. 1988). A single specimen was then collected at San Marcos Springs (Barr 1993). CSRBs are now known from Comal Spring runs No. 1, No. 2, and No. 3; at several spring outflows and seeps along the northwestern shore of Landa Lake; and near springs in Landa Lake and on Spring Island. Adults and larvae have been collected at San Marcos Springs from the springs along the escarpment near the Texas Rivers Center and in locations in upper Spring Lake, indicating the presence of a reproducing population (Gibson et al. 2008). Efforts to verify the presence of the species from other springs in central Texas have failed to locate any individuals beyond those associated with Comal and San Marcos Springs. Based on the best available scientific and commercial information, we estimate a total surface population of 10,959 individuals in the Comal Springs system, but cannot estimate populations in the San Marcos system (Bowles et al. 2003, Gibson 2011)(see Figure 2 and Table 3). Over half of this Comal Springs population is estimated to occur in Comal Spring runs No. 1 and No. 2. About 39 percent of the population is estimated to occur in in Comal Spring run No. 3.

Reasons for Decline and Threats to Survival

The listing rule describes reduction or loss of water of adequate quality and quantity as the main threat to the CSRB, and States that this decline is due primarily to human activities including withdrawal of water from the San Antonio segment of the Edwards Aquifer (62 FR 66295). The limited amount of available habitat is likely to be impacted or lost through drying or decreased volume of spring flow during drought conditions.

The CSRB is only known from two locations, and the flightless aquatic beetle has limited opportunities to expand its range. The species is therefore presumed to have survived the DOR at Comal Springs and San Marcos Springs, though because the species was first collected in 1976 there are no records of species abundance and distribution before, during, or for decades after the DOR event.

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the result of a catastrophic event such as a hazardous material spill or other release within the watershed or into Landa Lake, Spring Lake or their immediate tributaries constitutes another threat to the species. Landa Lake and its immediate tributaries are crossed by a total of five bridges, and Spring Lake and its immediate tributaries are crossed by a total of four bridges, any of which could be the source of a spill that could affect the species or its designated critical habitat units at Comal and San Marcos Springs. Stormwater inflows and other non-point sources of contamination may also pose a threat to the species.

Stagnation of water or drying within the occupied springs and spring runs may adversely affect the CSRB because flowing water with sufficient dissolved oxygen concentrations is considered important to respiration and therefore survival for this species.

Competition is not known to be a significant threat to this species, though the presence of non native species (such as the snails Marisa cornuarietis, Thiara granifera and Thiara tuberculata present in the spring runs) that may compete directly or indirectly for food resources have been identified as an ongoing threat to the continued survival of the CSRB (62 FR 66295).

This environmental baseline describes the current status of the species and is based upon impacts to which the species has been exposed (Service and NMFS 1998). To understand the potential effects of the Edwards Aquifer management under the HCP, modelers used pumping amounts as managed by the EAA CPM plan and measures planned to reduce Edwards Aquifer demand. They simulated Comal and San Marcos springflows a 54-year period (1947 through 2000) that included the DOR event (1949 to 1956) (HDR Engineering, Inc. et al. 2011). The reduction and loss of springflows projected by these modeling efforts during severe drought conditions could have significant impacts to the CSRB.

Survival Needs and Recovery Criteria

The chief survival need of the CSRB identified in the listing rule is conservation of suitable habitat to sustain populations of the species. The conservation of CSRB habitat includes maintenance of water quality and continuous natural springflow at Comal and San Marcos springs. No recovery plan has been finalized for the CSRB at this time, though a recovery team has been convened and a recovery plan that will include recovery criteria is currently being drafted.

Factors affecting the Species within the Action Area

The CSRB has been the subject of five formal consultations for Federal actions unrelated to the action considered here. The USACE consulted three times with the Service for flood damage repairs, bank stabilization, and bridge repairs. The Service completed an intra-Service consultation regarding the pumping of Edwards Aquifer water that supports the continuing operations and refugia of the San Marcos National Fish Hatchery and Technology Center and the Uvalde National Fish Hatchery. The incidental take of 302 CSRBs was authorized in conjunction with these four consultations. None of these consultations resulted in a determination that the considered actions would jeopardize the CSRB or result in destruction or adverse modification of designated critical habitat.

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In January 2013, the Service completed an intra-Service consultation regarding the issuance of incidental take permit (ITP), subsequently issued on March 18, 2013, for the CSRB (and other Edwards dependent animal species) to the EARIP applicants: EAA, City of New Braunfels, City of San Marcos, SAWS, and Texas State University (TSU). The ITP authorized the incidental take of no more than 11,179 CSRBs.

On April 27, 2012, the Texas Parks and Wildlife Commission amended the State List of Endangered Species (31 TAC §65.176) to include the CSRB (Texas Register 2012). Section 68.002 of the TPW Code and § 65.171 of the TAC prohibit take of endangered species, except under a State Scientific Research or Non-game Collection Permit. ‘‘Take’’ is defined in § 1.101(5) of the TPW Code as to collect, hook, hunt, net, shoot, or snare, by any means or device, and includes an attempt to take or to pursue in order to take. There are no provisions under the Texas Threatened and Endangered Species Regulations for reducing or eliminating the threats that may adversely affect the CSRB or its habitat.

Critical Habitat

Critical habitat for the CSRB was designated on July 17, 2007 in two units, referred to as the Comal Springs Unit and the San Marcos Springs Unit (72 FR 39248). Both of these units are located within the action area for this consultation.

Designated critical habitat for the CSRB in the Comal Springs Unit includes aquatic habitat within Landa Lake and outlying spring runs that occur from the confluence of Blieders Creek at the upstream end of Landa Lake down to the lake’s lowermost point of confluence with Spring run No. 1. The San Marcos Springs unit includes aquatic habitat areas within Spring Lake upstream of Spring Lake dam, with the exception of the slough portion of the lake upstream of its confluence with the main body.

Primary threats to designated critical habitat may vary for individual springs according to the degree of urbanization and availability of aquifer source water, but possible threats generally include prolonged cessation of spring flows as a result of the loss of hydrological connectivity within the aquifer (e.g., groundwater pumping, excavation, concrete filling), pollutants (e.g., stormwater drainage, pesticide use), and non-native species (e.g., biological control, sport fish stocking). Management actions may be required to address these threats; for example, maintenance of sustainable groundwater use and subsurface flows, use of adequate buffers for water quality protection, selection of appropriate pesticides, and implementation of integrated pest management plans.

The primary constituent elements identified in the critical habitat designation for the Comal Springs dryopid beetle are:

CSRB PCE 1. High-quality water with no or minimal levels of pollutants, such as soaps and detergents and other compounds containing surfactants, heavy metals, pesticides, nutrients, petroleum hydrocarbons, pharmaceuticals and veterinary medicines, and semi-volatile compounds, such as industrial

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cleaning agents, and including: (a) Low salinity with total dissolved solids that generally range from 307 to 368 mg/L; and, (b) Low turbidity of generally less than 5 nephelometric turbidity units; CSRB PCE 2. Aquifer water temperatures that range from approximately 68 to 75°F (20 to 23.9°C); CSRB PCE 3. A hydrologic regime that allows for adequate spring flows that provide levels of dissolved oxygen in the approximate range of 4.0 to 10.0 mg/L; CSRB PCE 4. Food supply that includes detritus (decomposed materials), leaf litter, living plant material, algae, fungi, bacteria and other microorganisms, and decaying roots; and, CSRB PCE 5. Bottom substrate in surface water habitat that is free of sand and silt, and is composed of gravel and cobble ranging in size between 0.3 to 5.0 inches (0.76 to 12.7 cm).

Both the Comal Springs and San Marcos Springs designated critical habitat units currently provide the primary constituent elements identified as essential for the conservation of the species. Water quality at both sites remains free from contamination and salinity and turbidity are within the described parameters. Water temperature averages approximately 74°F (23.3°C) in the Comal Springs system, and 70°F (21.1°C) at San Marcos Springs. Springflows continue to maintain dissolved oxygen levels at both locations, and food supplies are present. Bottom substrates in the designated critical habitat unit in the Comal system remain largely free of sand and silt. Substrates in Spring Lake have been impacted by sediments to a greater degree.

The Service proposed a revision to CSRB critical habitat on October 19, 2012 (77 FR 64272). The PCE of the proposed critical habitat is nearly identical to the designated CSRB PCE except the first PCE includes the following: “hydrologic regimes similar to the historical pattern on the specific sites, with continuous surface flow for the spring sites and in the subterranean aquifer”. The proposed critical habitat units for Comal Springs and San Marcos Springs include a critical habitat subsurface area that extends 50 feet horizontally from the critical habitat surface area for both Comal and San Marcos units. The proposed revisions to CSRB critical habitat are discussed further below in Section 8.

3.e. San Marcos Gambusia

The entire range of the San Marcos gambusia (Gambusia georgei) falls within the action area and this species description therefore constitutes the environmental baseline for this species.

Species Description and Life History

The San Marcos gambusia (SMG) was described from the upper San Marcos River system in 1969, and was subsequently listed as endangered on July 14, 1980 (45 FR 47355). Of the three species of Gambusia native to the San Marcos River, SMG has apparently always been much less abundant than either the largespring gambusia (G. geiseri) or the western mosquitofish (G. affinis) (Hubbs and Peden 1969).

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The SMG is a member of the family Poeciliidae and belongs to a genus of Central American origin having more than 30 species of livebearing freshwater fishes. The genus Gambusia is well defined and mature males may be distinguished from related genera by their thickened upper pectoral fin rays (Rosen and Bailey 1963). Only a limited number of species of Gambusia are native to the United States, and of these the SMG has (had) one of the most restricted ranges.

The food habits of SMG are unknown. Presumably, as in other poeciliids, insect larvae and other invertebrates account for most of the diet of this species.

There is little information on the reproductive capabilities of SMG. Two individuals kept in laboratory aquaria produced 12, 30, and 60 young, although the largest clutch appeared to have been aborted and did not survive (Edwards et al. 1980).

Hybridization between SMG and G. affinis was first noted by Hubbs and Peden (1969) and the production of hybrid individuals between them has continued for many years without obvious introgression of genetic material into either of the parental species. Given the history of hybridization between these two species, this factor was not thought to be of primary importance in considerations of the status of SMG. It was thought that so long as the proportion of hybrids remained relatively low compared to the abundance of pure SMG, few problems associated with genetic swamping or introgression would occur (Hubbs and Peden 1969, Edwards et al. 1980). However, the series of collections (R.J. Edwards, pers. comm.) taken during 1981 - 1983 indicate that hybrid individuals may have become many times more abundant than the pure SMG. It may have been possible that hybrid individuals at that time were competing with SMG, placing an additional stress on the small native population of SMG.

The SMG apparently prefers quiet waters adjacent to moving water, but seemingly of greatest importance, thermally constant waters. SMG is found mostly over muddy substrates but generally not silted habitats, and shade from over-hanging vegetation or bridge structures is a factor common to all sites along the upper San Marcos River where apparently suitable habitats for this species occur (Hubbs and Peden 1969, Edwards et al. 1980).

Historic and Current Distribution

The SMG is represented in collections taken in 1884 by Jordan and Gilbert during their surveys of Texas stream fishes and in later collections (as a hybrid) taken in 1925 (Hubbs and Peden 1969). Unfortunately, records of exact sampling localities are not available for these earliest collections, as localities were merely listed as “San Marcos Springs.” These collections likely were taken at or near the headsprings area. If true, then SMG appears to have significantly altered its distribution over time. For the area of the San Marcos River downstream of the headwaters area, there are few records of sampling efforts prior to 1950. However, even in the samples that were taken there are few collections of SMG.

A single individual was taken in 1953 below the low dam at Rio Vista Park. Almost every specimen of SMG collected since that time, however, has been taken in the vicinity of the Interstate Highway 35 Bridge crossing or shortly downstream. The single exception to this was a

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male captured accidentally with an Ekman dredge (sediment sampler) about 0.62 miles below the outfall of the San Marcos wastewater treatment plant in 1974 (Longley 1975).

Historically, SMG populations have been extremely sparse. Intensive collections during 1978 and 1979 yielded only 18 SMG from 20,199 Gambusia total (0.09 percent) (Edwards et al. 1980). Collections made in 1981 and 1982 within the range of SMG indicated a slight decrease in relative abundance of this species (0.06 percent of all Gambusia) and none have been collected in subsequent sampling from 1982 to the present. Intensive searches for SMG were conducted in May, July, and September of 1990 but were unsuccessful in locating any pure SMG. The searches consisted of a total of 18 hours of effort (more than 180 people-hours) on three separate days and covered the area from the headwaters at Spring Lake to the San Marcos wastewater treatment plant outfall. Over 15,450 Gambusia were identified during the searches. One individual collected during the search was visually identified as a possible backcross of G. affinis and SMG (Service 1990 permit report). This individual was an immature fish with plain coloration. Additional sampling near the Interstate Highway 35 type locality has occurred at approximately yearly intervals since 1990 and no SMG have been found.

The Service and cooperators conducted five fish collections in the upper San Marcos River during the period 1994 and 1996. Edwards (1999) identified 32,811 Gambusia in collection jars from that effort. No SMG were found and Edwards concluded this species appears to be extinct.

The pattern of SMG abundance strongly suggests a decrease beginning prior to the mid-1970s. The increase in hybrid abundance between SMG and G. affinis and the decrease in the proportion of genetically pure SMG is considered evidence of its rarity. As fewer pure individuals encountered each other, the chances of hybridization with the much more common G. affinis substantially increased. The subsequent decrease in SMG abundance along with their hybrids suggests the extinction of this species.

Reasons for Decline and Threats to Survival

At the time the species was listed, small and declining populations, lowered water tables, pollution, bottom plowing, and cutting of vegetation were cited as threats to the species (Service 1980).

Groundwater depletion, reduced springflows, contamination, habitat impacts resulting from severe drought conditions, and cumulative effects of human activities are all identified as threats to the species throughout all or a significant portion of its range (Service 1978, 1980).

Water quality is believed to be important to the SMG. Groundwater contamination or pollution resulting from a catastrophic event such as a hazardous material spill into the San Marcos River constitutes another threat to the species. The upper San Marcos River and its immediate tributaries are crossed by a total of 30 bridges including four railroad bridges and six associated

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with Interstate Highway 35. Any of these river crossings could be the source of a spill or release that could affect the species or its designated critical habitat in the San Marcos River. Stormwater inflows and other non-point sources of contamination may also pose a threat to the species.

Recreational use of the San Marcos River can also result in adverse impacts to the SMG or its habitat. Recreational uses that physically alter habitats may affect the species ability to feed and shelter.

Non-native species may threaten the SMG though habitat disturbance, or alteration. The SMG inhabits open areas with little vegetation. Suckermouth catfishes (Loricaridae) introduced into the San Marcos River disrupt substrates and may burrow into and destabilize riverbanks, thereby introducing additional sediment loads and turbidity into the river systems. Some researchers have hypothesized that the non-native plant Elephant ears (Colocasia esculenta) may have adversely affected SMG habitat suitability (Service 1996a).

Sediment and sand bar accumulations that modify the river channel and associated habitats may also impact the species or its designated critical habitat. These sediment loads may be associated with the increasing urbanization of the lands surrounding the upper San Marcos River.

The apparent demise of the SMG may be attributed in part to Allee effects, which become important in small populations. The few SMG present in the early 1980s were unlikely to find mates and reproduction rates likely went from rare to zero.

Survival Needs and Recovery Criteria

The SMG apparently requires thermally constant water; quiet, shallow, open water adjacent to moving water; muddy substrates without appreciable quantities of silt; partial shading; clean and clear water; and a food supply of living organisms.

Elephant ears (Colocasia esculenta) are a non-native emergent macrophyte believed to have been introduced into the San Marcos area in the early 1900s (Akridge and Fonteyn 1981). This species has displaced native vegetation and now form extensive stands at the water’s edge in the San Marcos system. Although the exact nature of the relationship between the occurrence and abundance of elephant ears and the disappearance of SMG is unknown, some investigators believe these nonnative plants may have decreased habitat suitability and contributed to its decline (Service 1996a).

Academic researchers, Texas Parks and Wildlife Department scientists, and the Service have continued to search for the species in the San Marcos River. The last confirmed collection of the species was reported in 1982 (Service 1996a).

Factors affecting the Species within the Action Area

The SMG has been the subject of two formal consultations for Federal actions unrelated to the action considered here. We consulted with USACE on a new stormwater outfall to the San

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Marcos River. The Service completed an intra-Service consultation (January, 2013) regarding the issuance of incidental take permit (ITP)(March 18, 2013) for the CSRB (and other Edwards dependent animal species) to the EARIP applicants: EAA, City of New Braunfels, City of San Marcos, San Antonio Water System (SAWS), and Texas State University (TSU). The ITP did not provide incidental take SMG.

We determined the proposed action would not jeopardize the San Marcos gambusia nor result in destruction or adverse modification of designated critical habitat.

On May 15, 1976, the Texas Parks and Wildlife Commission placed the SMG on the State list of endangered species (Texas Register 2010). Section 68.002 of the TPW Code and § 65.171 of the Texas Administrative Code (TAC) prohibit take of an endangered species, except under a State Scientific Research or Non-game Collection Permit. ‘‘Take’’ is defined in § 1.101(5) of the TPW Code as to collect, hook, hunt, net, shoot, or snare, by any means or device, and includes an attempt to take or to pursue in order to take. There are no provisions under the Texas Threatened and Endangered Species Regulations for reducing or eliminating the threats that may adversely affect the SMG or its habitat.

Critical Habitat

Designated critical habitat for the SMG is described as the San Marcos River from Highway 12 Bridge downstream to approximately 0.5 miles below Interstate Highway 35 Bridge (45 FR 47355). The designated critical habitat for the SMG is wholly contained within the described action area for this consultation.

The rule-making for the SMG predates the October 1, 1984, regulation (49 FR 38900) stipulating that primary constituent elements (PCEs) essential for the conservation of the species be identified at the time critical habitat is designated. However, the rule describes actions that would adversely modify designated critical habitat, including those that would result in an increase in vegetation in the species’ preferred open areas with little current away from stream banks, disrupt the mud bottom, or alter the temperature regime. Based on the best available scientific and commercial data available, the primary constituent elements could generally be defined as:

SMG PCE 1. Open areas with little current or vegetation away from stream banks; SMG PCE 2. Maintenance of natural substrates; and SMG PCE 3. A natural temperature regime in occupied areas of the San Marcos River.

The designated critical habitat in the San Marcos River generally provides the primary elements considered essential for the conservation of the SMG. The San Marcos River provides a mixture of aquatic habitats including open areas away from stream banks with little vegetation. Bottom substrates in the designated critical habitat unit in the San Marcos River have been impacted by siltation and sediments, though areas with natural substrates still exist. Water temperature in the San Marcos River remains within the ranges of 68.7°F in February to 77.9°F in August (Vaughan 1986).

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3.f. Fountain Darter

The entire range of the fountain darter (Etheostoma fonticola) is within the action area, and this status of the species therefore constitutes the environmental baseline for this species.

Species Description and Life History

The fountain darter was listed under the Endangered Species Conservation Act of 1969 on October 13, 1970 (35 FR 16047), in Appendix D – United States List of Endangered Native Fish and Wildlife. After the Endangered Species Act of 1973 superseded earlier endangered species statues, the fountain darter was again listed as an endangered species on September 26, 1975 (40 FR 44412).

The fountain darter is a small (adults average slightly larger than 1 inch total length), benthic, reddish brown fish (Page and Burr 1979). There are about eight stitch-like marks along the sides (Jordan and Evermann 1896).

Fountain darters spawn year-round (Schenck and Whiteside 1977b). Some authors have described two peak spawning periods, one in August and another late winter to early spring (Schenck and Whiteside 1977b), while others have suggested that fountain darter reproduction may be tied to habitat quality (BIO-WEST 2007). Some data supports year-round reproduction in areas of high-quality habitat in both the Comal and San Marcos systems (e.g., Spring Lake, Landa Lake), with a strong spring peak in reproduction (with limited reproduction in summer and fall of most years) in areas of lower quality habitat farther downstream (BIO-WEST 2007).

Fountain darter eggs have been found attached to bryophytes and algae in Spring Lake and on filamentous algae Rhizoclonium sp., Ludwigia repens, Sagittaria sp., and TWR in the San Marcos River (Dowden 1968, Phillips and Alexander unpublished data). After hatching, fry are not free swimming, in part due to the reduced size of their swim bladders.

Fountain darters prefer undisturbed stream floor habitats; a mix of submergent plants (algae, mosses, and vascular plants), in part for cover; clear and clean water; an invertebrate food supply of living organisms (copepods, dipteran (fly) larvae, and mayfly larvae); constant water temperatures within the natural and normal river gradients; and adequate springflows (Bergin 1996, Schenck and Whiteside 1977a). Fountain darter densities are lower in areas lacking vegetation (Institute of Natural Systems Engineering 2004, BIO-WEST 2013).

Historic and Current Distribution

The fountain darter was historically found in the Comal and upper San Marcos rivers (Service 1996a). The type specimens were collected from the San Marcos River immediately below the confluence with the Blanco River in 1884 (Jordan and Gilbert 1886). The first records from the Comal River consisted of 43 specimens collected in 1891 (Evermann and Kendall 1894).

The fountain darter is known to have been present in the San Marcos River from the headwaters (including Spring Lake) downstream to the vicinity of Martindale in Caldwell County (Service

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1996a). Fountain darters can currently be found Spring Lake to a point between the San Marcos Waste Water Treatment Plant (WWTP) outfall and the confluence with the Blanco River (Service 1996b). Researchers have estimated the San Marcos River population of the fountain darter to total 45,900 individuals (downstream of and excluding Spring Lake) (Linam 1993), to as many as 103,000 (Schenck and Whiteside 1976). Fountain darter densities appear to be highest in the upper segments of the San Marcos River and decrease markedly in an area below Cape's Dam (Linam 1993, Whiteside et al. 1994).

The fountain darter population was extirpated from the Comal River system in the mid-1950s (Schenk and Whiteside 1976). In 1954, rotenone was applied to the Comal system to remove non-native and exotic fish, and fountain darter populations may have been adversely impacted to an unknown degree by this effort (Ball et al. 1952, Service 1996a). The primary cause of extirpation, however, is thought to be the 1949-1956 DOR. The most likely cause of the extirpation of the fountain darter in the Comal River system was the cessation of Comal Springs flows for 144 days from June to November, 1956 (Schenck and Whiteside 1976). This event likely resulted in significant temperature fluctuations in remaining pools of water, decreased habitat and water quality, and increased predation of fountain darters.

Intensive surveys from 1973 to 1975 were unable to verify presence of the species in the Comal River system. From February 1975 through March 1976 about 450 fountain darters collected from the San Marcos River were released into the headsprings of the Comal River and into the old Comal River channel. By June of 1976, five offspring were found a short distance below the headsprings, confirming recruitment and re-establishment of a population (Schenck and Whiteside 1976). Fountain darters now occupy Comal Springs and the Comal River from Landa Lake downstream to the confluence with the Guadalupe River. A 1990 survey estimated that the Comal River population totaled about 168,078 individuals between the headwater springs and Clemens Dam (Linam et al. 1993).

The fountain darter occupies virtually all of the Comal River and most of the San Marcos River above the confluence of the San Marcos River and Blanco River. In The Comal River system, the only habitats not likely to support fountain darters are the upper reach of Spring run 2, which has little vegetation. In the case of Spring run 2, the wading pool weir acts as a fish barrier. One factor that degrades the fountain darter habitat in lower Spring run 1 and the embayment of Landa Lake is the intense herbivory by non-native (and native) waterfowl, which has eliminated most rooted macrophytes and reduced fountain darter habitat suitability.

The Service and cooperators surveyed for fountain darters in the action area from July 1993 to April 1994, and in July 1996 (Service 1996b). The fountain darter abundances in Spring runs 1, 2, and 3 were low compared to nearby habitat in Landa Lake and Comal River new channel. Dammeyer (2010) conducted a mark and recapture study in the Comal River old channel and estimated the number of fountain darters in a 100 m section as 2,732. Assuming homogeneity of channel width, habitat quality, and fountain darter density throughout the Comal River old channel (the old channel is 2,550 m long), the fountain darter population in the old channel is estimated at 6,967.

The EARIP HCP (2012) used a STELLA® model to estimate fountain darter numbers in the

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Comal system for average to low springflow. The median (50th percentile) discharge for monthly springflow at Comal Springs is 295 CFS. For the U.S. Geological Survey’s period of record for Comal Springs (1932 to present), a discharge of 225 CFS falls near the 23rd percentile. At 225 CFS total springflow, the model estimates an average of 114,837 fountain darters (EARIP HCP 2012).

Current population estimates place the fountain darter population at about 774,000 individuals within the Comal River system (including Landa Lake). BIO-WEST estimates 480,000 individuals within the San Marcos River, and 455,400 individuals within the high quality habitat within Spring Lake (414,000 square feet with estimated fountain darter densities of 1.1 darter per square foot ) (BIO-WEST 2011).

Reasons for Decline and Threats to Survival

The San Marcos and Comal Springs and Associated Aquatic Ecosystems Recovery Plan identifies several threats to the fountain darter (Service 1996a). The primary threats are related to the quantity and quality of aquifer and spring water. Drought conditions, groundwater use, and lower than average springflows threaten the species recovery. Activities that may pollute the Edwards Aquifer and its springs and streamflows may also threaten the species. Additional threats include effects from increased urbanization near the rivers; recreational activities; habitat modification; predation, competition, and habitat alteration by non-native species; and the effects of introduced parasites (Service 1996a).

Fountain darters appear to be a pollution sensitive species and require high quality water, which is provided by the Edwards Aquifer. Groundwater contamination or pollution resulting from a catastrophic event such as a hazardous material spill into the Comal or upper San Marcos rivers constitutes another threat to the species. The Comal River and Landa Lake and their immediate tributaries are crossed by a total of 19 bridges including three railroad bridges; and the upper San Marcos River including Spring Lake and their immediate tributaries are crossed by a total of 30 bridges including four railroad bridges and six associated with Interstate Highway 35. Any of these river crossings could be the source of a spill or release that could affect the species or its designated critical habitat in the San Marcos River. Stormwater inflows and other non-point sources of contamination may also pose a threat to the species.

Recreational use of the San Marcos River can also result in adverse impacts to fountain darters. Recreation in the San Marcos River has been reported as seasonal, with the highest use during summer months, holidays and weekends (Bradsby1994). Recreational uses that physically alter habitats or that result in loss of aquatic vegetation, such as trampling or uprooting vegetation, may affect the fountain darter’s ability to feed and shelter. Fountain darters reproduce by adhering eggs to aquatic plants (Dowden 1968, Phillips and Alexander unpublished data). Impacts to vegetation that supports fountain darter eggs could affect breeding success.

Non-native species can threaten fountain darters though competition, habitat disturbance, and parasitic infection. Introduced fishes found in these river systems include tilapia (Cichlidae) that disrupt substrates thereby increasing turbidity and alter habitats by clearing areas of aquatic vegetation, thereby potentially affecting fountain darter sheltering and breeding habitats.

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Suckermouth catfishes (Loricaridae) disrupt substrates and may burrow into and destabilize riverbanks, thereby introducing additional sediment loads and turbidity into the river systems.

Another non-native species that threatens the fountain darter is a parasitic trematode that attacks the fish’s gills (Mitchell et al. 2000 and McDonald et al. 2006). The trematode is native to Southeast Asia, and is associated with the presence of a non-native snail in the Comal and San Marcos systems. The adverse effects of these parasites on their fountain darter hosts is believed to increase during stressful conditions associated with low flow rates (Cantu 2003 and McDonald et al. 2007), and the parasite’s adverse effects may have greater effects on younger fountain darter life-Stages (McDonald et al. 2006). Currently, the trematode is more prevalent in the Comal system. In the San Marcos system the parasite is somewhat localized to river reaches near IH-35. A concern is the potential spread of the trematode throughout this system (through movement of various fish, snails, and avian intermediate hosts) thus adversely affecting the entire San Marcos fountain darter population.

This environmental baseline describes the current status of the species and is based upon impacts to which the species has been exposed (Service and NMFS 1998). To understand the potential effects of the currently authorized and actual pumping amounts as managed by the existing EAA CPM plan, springflow was modeled for a 54-year period (1947 through 2000) that included a range of precipitation conditions including the DOR event that occurred from 1949 to 1956. The reduction and loss of springflows projected by these modeling efforts during severe drought conditions could have significant impacts to the fountain darter in both the Comal and San Marcos River systems. Survival Needs and Recovery Criteria

The San Marcos and Comal Springs and Associated Aquatic Ecosystems Recovery Plan (Service 1996a) that includes fountain darter, identifies specific recovery actions including ensuring adequate flows and water quality in the San Marcos River; maintenance of genetically diverse reproductive populations in captivity and creation of reintroduction techniques for use in the event of a catastrophic event; removal or reduction of threats due to non-native species, recreational use of the river, and habitat alteration; and maintenance of healthy, self-sustaining, reproductive populations in the wild.

Factors affecting the Species within the Action Area

The fountain darter has been the subject of 10 formal consultations for Federal actions unrelated to the action considered here. The USACE consulted with the Service for a bank stabilization and retaining wall project, bridge repairs and removal of concrete footings from two bridges at Landa Lake, and repair and installation of erosion protection for a water pipeline that crosses the Comal River. The USACE consulted with the Service for projects that impact the San Marcos system, including a stormwater outfall and the replacement of two bridges over the San Marcos River, repairs to Spring Lake Dam, and an aquatic restoration project at Spring Lake. The Service also completed an intra-Service consultation regarding the pumping of Edwards Aquifer water that supports the continuing operations and refugia at the San Marcos National Fish Hatchery and Technology Center and the Uvalde National Fish Hatchery. The incidental take of up to 4,858 fountain darters was authorized under these nine consultations. We determined that

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the proposed action would not jeopardize the fountain darter or adversely modify its critical habitat.

The Service completed an intra-Service consultation regarding the issuance of incidental take permit (March 18, 2013) for the fountain darter (and other Edwards dependent animal species) to the EARIP permittees. The ITP authorized the incidental take of no more than 1,346,129 fountain darters (797,000 from the Comal River system and 549,129 from the San Marcos River system). The EA RIP HCP estimated that up to 95 percent of the Comal system fountain darter population (take of 735,000) could be lost during a repeat of DOR conditions. Similarly, under DOR conditions, the EA RIP HCP estimated the San Marcos River system may have losses (take) of up to 450,000 fountain darters. The authorized incidental take of fountain darters associated with severe drought conditions accounts for about 88 percent of all authorized incidental take. The remaining 12 percent is incidental to beneficial restoration measures that will occur only during periods of when discharge at Comal Springs exceeds 130 cfs and San Marcos Springs exceeds 120 cfs.

On May 19, 1974, the Texas Parks and Wildlife Commission placed the fountain darter on the State list of endangered species (Texas Register 1974). Section 68.002 of the TPW Code and Section 65.171 of the TAC prohibit take of an endangered species, except under a State Scientific Research or Non-game Collection Permit. ‘‘Take’’ is defined in Section 1.101(5) of the TPW Code as to collect, hook, hunt, net, shoot, or snare, by any means or device, and includes an attempt to take or to pursue in order to take. There are no provisions under the Texas Threatened and Endangered Species Regulations for reducing or eliminating the threats that may adversely affect the fountain darter or its habitat.

This designation authorizes the State natural resource agency to limit recreation within designated areas when San Marcos River flows fall below 120 cfs. The designation provides for continued recreational use of the waterway by maintaining open channels outside of protection zones that run the length of the river. These areas allow for continued use of the river even during low flow periods for activities such as tubing, canoeing, kayaking, and swimming.

The regulation makes it unlawful to move, deface, or alter any signage, buoys, booms, or markers delineating the boundaries of the State Scientific Area; to uproot TWR within the area; or to enter any such marked areas. The City of San Marcos and Texas State University have committed to install kiosks at key locations identifying access points, exclusion areas, and providing educational information about the State Scientific Area and the species and habitats they are intended to conserve.

This designation includes habitat utilized by the fountain darter, and this newly enacted regulation may provide some conservation value to the species by limiting impacts from

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recreation during periods of low flow in the San Marcos River. However, because the State Scientific Area has only recently been established, no information has yet been collected concerning effects to listed species including the fountain darter.

The TPWD has committed to establishing a State Scientific Area in the Comal River to conserve existing and restored fountain darter habitat, though such designation has not been enacted at the time of this writing. Critical Habitat

Critical habitat was designated on July 14, 1980, and consists of Spring Lake and its outflow and the San Marcos River to a point 0.5 mile (0.8 km) downstream of Interstate Highway 35 (45 FR 47355). All designated critical habitat for the fountain darter is contained within the action area for this consultation.

The rule-making for the fountain darter (FD) predates the October 1, 1984, regulation (49 FR 38900) stipulating that primary constituent elements (PCEs) essential for the conservation of the species be identified at the time critical habitat is designated. However, the rule designating critical habitat (45 FR 47362) does describe actions that would adversely modify designated critical habitat, including any actions that would: significantly reduce aquatic vegetation in Spring Lake and the San Marcos River, impound water, excessively withdraw water, reduce flow, and pollute the water. Based on the best available scientific and commercial data available, the primary constituent elements could generally be defined as:

FD PCE 1. Undisturbed stream floor habitats (including runs, riffles, and pools); FD PCE 2. A mix of submergent vegetation (algae, mosses, and vascular plants); FD PCE 3. Clear and clean water; FD PCE 4. A food supply of small, living invertebrates; FD PCE 5. Relatively constant water temperatures associated with a natural spring-fed river; and FD PCE 6. Adequate spring flows to maintain the conditions above.

The designated critical habitat in Spring Lake and the upper San Marcos River today provides all of the primary elements considered essential for the conservation of the fountain darter. The San Marcos River provides a mixture of aquatic habitats including riffles, runs, and pools with a mixture of submergent vegetation, and suitable fountain dater food resources are available.

While the water in Spring Lake is exceptionally clear, Groeger et al. (1997) noted a gradient of increasing turbidity going downstream. Activities that contribute sediment loads, such as non- point source erosion from the urbanizing areas surrounding the upper San Marcos River, or activities that suspend existing sediments such as lake bottom disturbances by SCUBA divers in Spring Lake or swimmers in the San Marcos River, can increase turbidity and impact this element. Such turbidity in Spring Lake and the San Marcos River usually dissipate as the suspended particulates flow downstream or settle out of the water column in relation to flow rate. Continual or repeated re-suspension of particulates can markedly reduce water clarity. This can be observed downstream of popular recreation sites in the river during periods of intense use, including weekends and holidays.

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Temperature at San Marcos Springs reportedly varies less than 0.9°F near the headwater springs (Guyton and Associates 1979). Groeger et al. (1997), Slattery and Fahlquist (1997), and Saunders et al. (2001) reported an increasing range of water temperature going downstream from Spring Lake in the San Marcos River.

Flow rate is the result of precipitation and recharge that contribute to aquifer levels as they are affected by pumping throughout the region. Current aquifer management regulations limit pumping during drought conditions by specified amounts triggered by index well levels and springflows. These mechanisms have maintained continual springflows since they were enacted, though drought conditions during this time period have not approached the severity and duration of the DOR.

3.g. San Marcos salamander

The entire range of the San Marcos salamander (Eurycea nana) is within the action area, and this status of the species therefore constitutes the environmental baseline for the species.

Species Description and Life History

The San Marcos salamander (SMS) was listed as threatened on July 14, 1980 (45 FR 47355). This dark reddish brown slender salamander reaches lengths of one to two inches (2.5 to 5 cm), and has moderately large eyes with a dark ring around the lens. The species has well developed and highly pigmented gills, relatively short, slender limbs with four toes on the fore feet and five on the hind feet. SMS have a slender tail with a well-developed dorsal fin (Service 1996a).

The SMS is a member of the family Plethodontidae (lung-less salamanders) and is a neotenic salamander that retains its external gills (the larval condition) throughout life (Bishop 1941). The salamander does not leave the water to metamorphose into a terrestrial form, but instead becomes sexually mature and breeds in the water. Most evidence suggests reproduction occurs throughout the year with a possible peak about May and June (Service 1996a).

Habitat consists of algal mats (Tupa and Davis 1967), where rocks are associated with spring openings (Nelson 1993). Sandy substrates devoid of vegetation and muddy silt or detritus-laden substrates with or without vegetation are apparently unsuitable habitats for this species. Specimens are occasionally collected from beneath stones in predominantly sand and gravel areas. In view of the abundance of predators (primarily larger fish, but also crayfish, turtles, and aquatic birds) in the immediate vicinity of spring orifices, protective cover such as that afforded by algal mats and rocks is essential to the survival of the salamander. The flowing spring waters in the principal habitat are near neutral (pH 6.7-7.2), range from 69.8-73.4°F (21 to 23°C), clear, and dissolved oxygen levels are low (less than 50 percent saturated, 3-4 mg/L (Tupa and Davis 1967, Najvar 2001, Guyton and Associates 1979, Groeger et al. 1997).

Prey items for the SMS include amphipods, tendipedid (midge fly) larvae and pupae, other small insect pupae and naiads (an aquatic life stage of mayflies, dragonflies, damselflies, and stone flies), and small aquatic snails (Service 1996a).

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Historic and Current Distribution

A total of 20 SMS were collected from San Marcos Springs on 22 June 1938 (Bishop 1941). Subsequent researchers found the species near all of the major spring openings scattered throughout Spring Lake and downstream as far as 500 feet below Spring Lake dam (Tupa and Davis 1976, Nelson 1993, BIO-WEST 2010).

Population estimates for the SMS have ranged from 17,000 to 21,000 individuals in the floating algal mats at the uppermost portion of Spring Lake (Tupa and Davis 1976), to as many as 53,200 salamanders from Spring Lake and the rocky substrates within approximately 500 feet (152 meters) downstream of the Spring Lake Dams (Nelson 1993). Seven-years of quarterly monitoring of SMS populations using visual surveys by divers showed stable visual counts (BIO-WEST 2010).

One difficulty in estimating SMS populations is the small size of young salamanders and their ability to move undetected into interstitial spaces among the substrate. Tupa and Davis (1976) and Nelson (1993) estimated the number of SMS in and near Spring Lake and found them distributed throughout Spring Lake among rocks near spring openings, in algal mats, mosses, and other plants, and in rocky areas just downstream from the dams (Nelson 1993; BIO-WEST 2007, 2010). The species occurs near all of the major spring openings scattered throughout Spring Lake and is abundant at some of these springs (Nelson 1993). Nelson (1993) estimated a total population of 53,200 salamanders in and just below Spring Lake, including 23,000 associated with algal mats, 25,000 among rocky substrates around spring openings, and 5,200 in rocky substrates below Spring Lake.

SMS density estimates are based on sampling conducted 21 times since the fall of 2000 indicate that the size of the current salamander population appears to be thriving and generally similar to observations made over the previous eight-years of sampling (BIO-WEST 2010).

Reasons for Decline and Threats to Survival

The primary threats to the SMS are related to the quality and quantity of aquifer and spring water. The restricted distribution of the species, loss of protective cover, contaminants, siltation, and introduced predators may also threaten the species (45 FR 47355, Service 1996a).

Groundwater contamination or pollution resulting from a catastrophic event such as a hazardous material spill into Spring Lake or one of its tributaries could threaten the SMS or its designated critical habitat. Spring Lake, its tributaries, and the portion of the San Marcos known to be occupied by the species are crossed by six bridges. Stormwater and other non-point sources could also contribute pollutants that could threaten the species or affect its habitat.

Sediment and siltation in Spring Lake and the uppermost portions of the San Marcos River may also impact the species or its habitat. These sediment loads may be associated with the increasing urbanization of the lands surrounding the upper San Marcos River.

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When total maximum permitted pumping under current regulations is modeled, San Marcos Springs are projected to cease flowing for 30 consecutive days. For comparison purposes, San Marcos Springs are not reported to have ever stopped flowing, even during the DOR event. This projected model result, though useful in understanding potential effects of the existing aquifer management scheme, does not reflect impacts that the species have experienced because these conditions have not occurred since this management plan was adopted.

The reduction of San Marcos springflows projected during times of severe drought could affect the SMS, particularly those associated with the Spring Lake Dam spillways.

Survival Needs and Recovery Criteria

The SMS recovery needs are addressed in the San Marcos and Comal Springs and Associated Aquatic Ecosystems Recovery Plan (Service 1996a). Recovery tasks identified in the plan include: ensuring adequate flows and water quality in San Marcos Springs and the San Marcos River; maintenance of genetically diverse reproductive populations in captivity and creation of reintroduction techniques for use in the event of a catastrophic event; removal or reduction of threats due to non-native species, recreational use of the river, and habitat alteration; and maintenance of healthy, self-sustaining, reproductive populations in the wild.

The Service’s San Marcos Aquatic Resource Center (formerly the San Marcos National Fish Hatchery and Technology Center) has developed captive breeding techniques for SMS in the event that the natural population at San Marcos Springs is lost. The facility successfully produced more than 5,000 eggs by 2009, with an average hatch success at about 20 percent. Reproduction of this species, however, remains unpredictable (J. N. Fries, 2009, pers. obs., Service, San Marcos, Texas). Techniques for maintaining this species’ genetic diversity have been improved over the past several years. The ability to maintain this species in captivity (without supplemental wild caught individuals) over the long-term remains uncertain (Fries 2002). Reintroduction techniques have yet to be developed.

Factors affecting the Species within the Action Area

The SMS has been addressed in four formal consultations for Federal actions unrelated to the action currently under consideration. The USACE consulted with the Service for repairs to Spring Lake Dam, and an aquatic restoration project at Spring Lake. The Service also completed an intra-Service consultation regarding the pumping of Edwards Aquifer water that supports the continuing operations and refugia at the San Marcos National Fish Hatchery and Technology Center and the Uvalde National Fish Hatchery. Lastly, the Service consulted on the issuance of the EARIP HCP ITP.

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The incidental take of 842 SMS was authorized under the first three of these consultations. None of these consultations resulted in a determination that the considered actions would jeopardize the species or result in destruction or adverse modification of designated critical habitat. The fourth consultation (EARIP HCP ITP) authorized incidental take of no more than 263,857 SMS.

On July 18, 1977, the Texas Parks and Wildlife Commission placed the SMS on the State list of threatened species (Texas Register 2010). Section 68.002 of the TPW Code and § 65.171 of the Texas Administrative Code (TAC) prohibit take of threatened species, except under a State Scientific Research or Non-game Collection Permit. ‘‘Take’’ is defined in § 1.101(5) of the TPW Code as to collect, hook, hunt, net, shoot, or snare, by any means or device, and includes an attempt to take or to pursue in order to take. There are no provisions under the Texas Threatened and Endangered Species Regulations for reducing or eliminating the threats that may adversely affect the SMS or its habitat.

The regulation makes it unlawful to move, deface, or alter any signage, buoys, booms, or markers delineating the boundaries of the State Scientific Area; to uproot TWR within the area; or to enter any such marked areas. The City of San Marcos and Texas State University have committed to install kiosks at key locations identifying access points, exclusion areas, and providing educational information about the State Scientific Area and the species and habitats they are intended to conserve.

This designation includes habitat utilized by the SMS, and this newly enacted regulation may provide some conservation value to the species by limiting impacts from recreation during periods of low flow in the San Marcos River. However, because the State Scientific Area has only recently been established, no information has yet been collected concerning effects to listed species including the SMS.

Critical Habitat

Critical habitat for the SMS was designated on July 14, 1980, and is described as: Spring Lake and its outflow, the San Marcos River, downstream approximately 164 feet (50 meters) below Spring Lake dam (45 FR 47362). All designated critical habitat for this species is within the action area considered in this consultation.

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The critical habitat designation for SMS predates the requirement for identification of primary constituent elements essential for the conservation of the species. However, the rule designating critical habitat (45 FR 47362) describes actions that would adversely modify designated critical habitat, including those that would: lower the water table; expose algal mats, leading to the desiccation of the species sole habitat; and disturb algal mats or the bottom of the lake, such as from SCUBA divers. Based on the best available scientific and commercial data, the primary constituent elements (PCE) could generally be defined as:

SMS PCE 1. Thermally constant waters; SMS PCE 2. Flowing water; SMS PCE 3. Clean and clear water; SMS PCE 4. Sand, gravel, and rock substrates with little mud or detritus; and SMS PCE 5. Vegetation or rocks for cover.

The designated critical habitat in Spring Lake and the upper San Marcos River today provides all of the primary elements considered essential for the conservation of the SMS.

Temperature at San Marcos Springs reportedly varies less than 0.9°F (0.5°C) near the headwater springs (Guyton and Associates 1979).

The water in Spring Lake and the San Marcos River is usually clear. Activities that contribute sediment loads, such as non-point source erosion from the urbanizing areas surrounding the upper San Marcos River, or activities that suspend existing sediments such as lake bottom disturbances by SCUBA divers in Spring Lake or swimmers in the San Marcos River, can increase turbidity and impact this element. Such turbidity in Spring Lake and the San Marcos River usually dissipate as the suspended particulates flow downstream or settle out of the water column in relation to flow rate. Continual or repeated re-suspension of particulates can markedly reduce water clarity. This can be observed downstream of popular recreation sites in the river during periods of intense use, such as during weekends and holidays (Bradsby 1994, Breslin 1997).

Though some siltation and sedimentation of natural substrates has occurred, sand, grave, and rock substrates with little mud or detritus are available. Vegetation and rocky cover is present in both Spring Lake, and rocky cover types predominate in the uppermost designated portions of the San Marcos River.

3.h. Texas blind salamander

The entire range of the Texas blind salamander (Eurycea rathbuni) is within the action area

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considered here, and the status of the species therefore constitutes the environmental baseline for the species.

Species Description and Life History

The Texas blind salamander (TBS) was listed as endangered on March 11, 1967 under the Endangered Species Preservation Act of 1966 (32 FR 4001). The species was subsequently incorporated into the list of species threatened with extinction on October 13, 1970 (35 FR 16047) after the passage of the Endangered Species Conservation Act of 1969, and was again confirmed as an endangered species on September 26, 1975 (40 FR 44412) after the Endangered Species Act of 1973 superseded the earlier endangered species statues.

The TBS is a smooth, unpigmented, stygobitic (obligate aquatic cave-adapted) species. Adults attain an average length of about 4.7 inches (12 cm) with a large, broad head, and reduced eyes. The limbs are slender and long with four toes on the fore feet and five toes on the hind feet (Longley 1978). The TBS is a neotenic species believed to be adapted to the relatively constant temperatures (69.8°F) of the water-filled subterranean caverns of the Edwards Aquifer in the San Marcos area (Longley 1978).

Juveniles have been collected throughout the year, making it likely that this species is sexually active year-round (Longley 1978). The species does not have reliable external characters that can be used to distinguish between the sexes (Service 1996a).

The TBS is an active predator. It moves its head from side to side as it searches for food and hunts by sensing water pressure waves created by prey in the still underground waters where it lives. Prey items include amphipods, blind shrimp (Palaemonetes antrorum), daphnia, small snails, and other invertebrates. Observations of captive individuals indicate that TBS feed indiscriminately on small aquatic organisms and do not appear to exhibit an appreciable degree of food selectivity.

Observations indicate that this salamander moves through the aquifer by traveling along submerged ledges and may swim short distances before spreading its legs and settling to the bottom of the pool (Longley 1978).

Historic and Current Distribution

The TBS was first collected in 1895 from an artesian well drilled to supply water to the U. S. Fish Commission Hatchery in San Marcos, Texas (Longley 1978). The species has subsequently been collected at several other locations within Hays County, including Ezell’s Cave, San Marcos Springs, Rattlesnake Cave, Primer’s Fissure, Texas State University’s artesian well, and Frank Johnson’s well (Russell 1976, Longley 1978, ). The species was collected at Wonder Cave in 1917 (Uhlenhuth 1921) (also known as Beaver Cave), though searches in 1977 and since have not found any salamanders. The known range of the TBS has not changed since listing in 1967.

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Reasons for Decline and Threats to Survival

Threats to the TBS identified in the San Marcos and Comal Springs and Associated Aquatic Ecosystems Recovery Plan (Service 1996a) include loss of springflows due to decreases in aquifer levels; water quality declines (including a loss of historically stable thermal conditions); human modifications (such as bank stabilization, dams, and landowner maintenance activities in waterways and on adjacent tracts of land) that have changed the historical magnitude and occurrence of episodic events such as flooding, and indirect impacts from surrounding development and urbanization; and introduction of non-native species.

This environmental baseline describes the current status of the species and is based upon impacts to which the species has been exposed (Service and NMFS 1998). To understand the potential effects of the currently authorized and actual pumping amounts as managed by the existing EAA CPM plan, springflow was modeled for a 54-year period (1947 through 2000) that included a range of precipitation conditions including the DOR event that occurred from 1949 to 1956. While the Edwards Aquifer MODFLOW model estimates monthly average discharge at San Marcos Springs, it does not inform us of what effects may be expected in the TBS habitat of the recharge and artesian zone in the San Marco area.

Springflows are a function of aquifer level, and the reduction and loss of springflows projected by these modeling efforts during severe drought conditions suggests lowered aquifer levels. Given the TBS’s apparent restriction to the waters of the aquifer in Hays County, these lowered aquifer levels may represent impacts to the species and its habitat.

Survival Needs and Recovery Criteria

Recovery tasks identified in the San Marcos and Comal Springs and Associated Aquatic Ecosystems Recovery Plan (Service 1996a) include: assuring adequate water levels and water quality in the aquifer, establishment of captive breeding populations with sufficient genetic integrity and development of reintroduction techniques, addressing local threats to water quality and quantity, and ensuring that self-sustaining populations of the species exist throughout its

Little is known about the population size or trends in population for this species and no reliable estimates are available. The species’ range has been hypothesized to be as small as 39 square miles beneath and near the city of San Marcos (Longley 1978).

Factors affecting the Species within the Action Area

The TBS has been the subject of two formal consultations for Federal actions unrelated to the action considered here. The Service completed an intra-Service consultation addressing the continuing operations and refugia at the San Marcos National Fish Hatchery and Technology Center and the Uvalde National Fish Hatchery. We determined the proposed action would not jeopardize the TBS. The Service consulted on the issuance of the EARIP HCP ITP. The EA RIP HCP permittees are authorized to incidentally take 10 TBS.

On May 19, 1974, the Texas Parks and Wildlife Commission placed the TBS on the State list of

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endangered species (Texas Register 2010). Section 68.002 of the TPW Code and § 65.171 of the Texas Administrative Code (TAC) prohibit take of an endangered species, except under a State Scientific Research or Non-game Collection Permit. ‘‘Take’’ is defined in § 1.101(5) of the TPW Code as to collect, hook, hunt, net, shoot, or snare, by any means or device, and includes an attempt to take or to pursue in order to take. There are no provisions under the Texas Threatened and Endangered Species Regulations for reducing or eliminating the threats that may adversely affect the TBS or its habitat.

Critical Habitat

Critical habitat has not been designated for the TBS.

3.i. Environmental Baseline Factors Shared by Species in Consultation

The primary baseline factor that the species in this consultation have in common is the Edwards Aquifer Recovery Implementation Program and its Habitat Conservation Plan (EARIP HCP). The EARIP HCP measures can be grouped into three efforts: minimization, mitigation, and restoration. Minimization measures reduce impacts and contributing to recovery of covered species (Critical Period Management, Voluntary Irrigation Suspension Program, and Aquifer Storage and Recovery, among others). Mitigation measures address impacts such as non-native plants and animals. Restoration measures contribute to and enhance species recovery by supporting refugia (ex situ conservation) at Federal Hatcheries and protection / monitoring of water quality. A more complete accounting of these measures is provided in Chapter 5 of the EARIP HCP and the Service’s biological opinion for the EARIP HCP (both available online).

The scale of EARIP HCP efforts is broad. There are local measures to promote recovery in San Marcos and New Braunfels and at Texas State University. There are aquifer-wide scale minimization measures that reduce the effects of regional droughts. The Service has previously stated in our biological opinion for JBSA (Service 2008) that a successful regional effort including all non-Federal Edwards Aquifer users is key to improving the status of species in this consultation. With the EARIP HCP and formal consultations in place, all Edwards Aquifer users, non-Federal and Federal, are for the first time collectively contributing to the recovery of the Edwards Aquifer-dependent species.

4. Effects of the Action

This section includes an analysis of the direct and indirect effects of JBSA Edwards Aquifer use on species and designated critical habitats.

The main effects considered here are the adverse impacts to the listed Edwards species and their critical habitats due to JBSA’s aquifer withdrawals and resulting decrease in springflows at Comal, Hueco, and San Marcos springs. Hydrogeologists have not fully researched nor resolved the source(s) that provide springflow to Fern Bank Springs. Fern Bank springflow may originate in part from the Edwards Aquifer based on groundwater dye traces conducted by EAA and others (Johnson et al. 2012). In addition to the Edwards Aquifer, Fern Bank Springs flow may

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also partly come from the Trinity aquifer, water associated from the Blanco River, or some combination of these sources (George Veni in litt. 2006).

Johnson et al. (2012) stated the geologic setting “suggests that a groundwater divide exists between Fern Bank and San Marcos springs”. If a groundwater divide fits this description, Fern Bank Springs may be subject to more local (in contrast to regional) factors affecting recharge and well withdrawal effects. If groundwater associated with Fern Bank Springs is not connected to the larger regional system associated with Comal and San Marcos springs, JBSA activities in Bexar County would not be expected to affect Fern Bank Springs or its associated community.

4.a. Factors to be Considered

Factors to be considered include:

i. The weather-dependent effects of the action; ii. The probability of drought and a repeat of DOR conditions; and, iii. The potential impacts of climate change. iv. The Edwards Aquifer modeling incorporating the DOR and Edwards Aquifer management as envisioned in the EARIP HCP.

The weather-dependent effects of the action

The effects of JBSA pumping depends on (interacts with) precipitation and recharge conditions throughout the region. The effects of the action, therefore, will be a function of precipitation regime and recharge conditions experienced over the duration of the 15-year permit.

For example, some JBSA activities and minimization measures taken during average or above average aquifer conditions (average precipitation and recharge) would not be expected to discernibly affect water levels in the Edwards Aquifer. Similarly, when the Edwards Aquifer levels are average or above, JBSA activities and minimization measures are not likely have an apparent effect on flow at Comal and/or San Marcos Springs. However, these same measures are expected to affect aquifer levels and springflows during drought conditions and in turn affect the considered species and their habitats.

Because the effects of the action are weather-dependent, the analysis of stressors, potential exposures, and resulting effects of the various measures are provided for both normal and drought conditions. For the purposes of this analysis, “normal” conditions are presumed to follow the average precipitation and recharge conditions observed over the periods of record for the respective springs.

The average springflow over the period of record for Comal Springs (1933 to 2011) is 290 cfs. The average springflow at San Marcos Springs for the period 1957 through 2011 is 174 cfs. The drought conditions analyzed here consist of a repeat of the recorded precipitation and recharge conditions experienced from 1949 through 1956 DOR during the 15-year duration of the permit. This seven-year drought is the longest period of severe drought in the region for which precipitation and corresponding springflow data is available. Drought of record-like conditions

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are referred to throughout the remainder of the document as “DOR conditions”.

The probability of drought and the recurrence of DOR conditions

The U.S. Congress recognized the challenges associated with forecasting and preparing for drought, and established the National Drought Policy Commission under the National Drought Policy Act of 1998 to ensure collaboration between different government agencies on drought- related issues. The work of the Commission culminated in the National Integrated Drought Information System (NIDIS) Act of 2006.

The NIDIS Act defined drought as “a deficiency in precipitation that leads to a deficiency in surface or subsurface water supplies (including rivers, streams, wetlands, ground water, soil moisture, reservoir supplies, lake levels, and snow pack); and that causes or may cause substantial economic or social impacts; or substantial physical damage or injury to individuals, property, or the environment” (NIDIS Act of 2006).

Though droughts are common in the region they are usually short in duration and intensity (Riggio et al. 1987). The most severe drought in the study area since precipitation record keeping began is the 8-year DOR event that occurred from 1949 through 1956 that resulted in the only known cessation of flow at Comal Springs.

Researchers have attempted to determine precipitation patterns prior to the historic record in order to compare the severity and frequency of the DOR with previous droughts. One researcher found that droughts of various lengths occurred 40 times between the years 1700 and 1979 (Mauldin 2003). Most droughts lasted for less than 1-year, and the average drought lasted for 1.8-years. Of the four droughts that lasted for 3-years or more, three occurred in the 1700s and the fourth was the 7-year DOR. Though six droughts were found to be more intense for shorter durations, the DOR was determined to be the most intense long-term drought during the studied period (Mauldin 2003). Other research concluded that the DOR was the most prolonged period of sustained drought for a 347-year study period (Therrell 2000). A recent projection of climate data based on dendrochronology techniques suggests that droughts lasting a decade or longer appear to be randomly distributed in Western and Central Texas throughout the reconstructed period of 1500 through 2008 (Cleaveland et al. 2011).

Our ability to forecast droughts, however, is confounded by the influence of multiple independent variables and the stochastic nature of these natural events. Recent attempts to generate regional and statewide patterns describe significant uncertainties when projecting future precipitation due to the influence of these complicated interrelated mechanisms (Jiang and Yang 2012). For the purposes of this analysis, therefore, we presume that a seven-year precipitation pattern mimicking conditions experienced during the DOR will occur at some time during the 15-year duration of the permit.

The potential impacts of climate change

Our analyses include consideration of ongoing and projected changes in climate. The terms “climate” and “climate change” are defined by the Intergovernmental Panel on Climate Change

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(IPCC). “Climate” refers to the mean and variability of different types of weather conditions over time, with 30-years being a typical period for such measurements, although shorter or longer periods also may be used (IPCC 2007a). The term “climate change” thus refers to a change in the mean or variability of one or more measures of climate (e.g., temperature or precipitation) that persists for an extended period, typically decades or longer, whether the change is due to natural variability, human activity, or both (IPCC 2007a).

Scientific measurements spanning several decades demonstrate that changes in climate are occurring, and that the rate of change has been faster since the 1950s. Based on extensive analyses of global average surface air temperature, the most widely used measure of change; the IPCC concluded that warming of the global climate system over the past several decades is “unequivocal” (IPCC 2007a). In other words, the IPCC concluded that there is no question that the world’s climate system is warming. Examples of other changes include substantial increases in precipitation in some regions of the world and decreases in other regions (for these and additional examples, see IPCC 2007a; Solomon et al. 2007). Various environmental changes (e.g., shifts in the ranges of plant and animal species, conditions more favorable to the spread of invasive species and of some diseases, changes in amount and timing of water availability) are occurring in association with changes in climate (see IPCC 2007a, Global Climate Change Impacts in the United States 2009).

Results of scientific analyses presented by the IPCC show that most of the observed increase in global average temperature since the mid-20th century cannot be explained by natural variability in climate, and is “very likely” (defined by the IPCC as 90 percent or higher probability) due to the observed increase in greenhouse gas (GHG) concentrations in the atmosphere as a result of human activities, particularly carbon dioxide emissions from fossil fuel use (IPCC 2007b, Solomon et al. 2007). Further confirmation of the role of GHG comes from analyses by Huber and Knutti (2011), who concluded that it is extremely likely that approximately 75 percent of global warming since 1950 has been caused by human activities.

Scientists use a variety of climate models, which include consideration of natural processes and variability, as well as various scenarios of potential levels and timing of GHG emissions, to evaluate the causes of changes already observed and to project future changes in temperature and other climate conditions (e.g., Meehl et al. 2007, Ganguly et al. 2009). All combinations of models and emissions scenarios yield very similar projections of average global warming until about 2030. Although projections of the magnitude and rate of warming differ after about 2030, the overall trajectory of all the projections is one of increased global warming through the end of this century, even for projections based on scenarios that assume that GHG emissions will stabilize or decline. Thus, there is strong scientific support for projections that warming will continue through the 21st century, and that the magnitude and rate of change will be influenced substantially by the extent of GHG emissions (IPCC 2007a, Meehl et al. 2007, and Ganguly et al. 2009).

In addition to basing their projections on scientific analyses, the IPCC reports projections using a framework for treatment of uncertainties (e.g., they define “very likely” to mean greater than 90 percent probability, and “likely” to mean greater than 66 percent probability; see Solomon et al. 2007). Some of the IPCC’s key projections of global climate and its related effects include:

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(1) it is virtually certain there will be warmer and more frequent hot days and nights over most of the earth’s land areas; (2) it is very likely there will be increased frequency of warm spells and heat waves over most land areas; (3) it is very likely that the frequency of heavy precipitation events, or the proportion of total rainfall from heavy falls, will increase over most areas; and (4) it is likely the area affected by droughts will increase, that intense tropical cyclone activity will increase, and that there will be increased incidence of extreme high sea level (IPCC 2007b). More recently, the IPCC published additional information that provides further insight into observed changes since 1950, as well as projections of extreme climate events at global and broad regional scales for the middle and end of this century (IPCC 2011).

Climate changes may have direct or indirect effects on species. These may be positive, neutral, or negative, and they may change over time, depending on the species and other relevant considerations, such as interactions of climate with other variables such as habitat fragmentation (for examples, see Franco et al. 2006, IPCC 2007a, Forister et al. 2010, Galbraith et al. 2010, Chen et al. 2011). In addition to considering individual species, scientists are evaluating possible climate change–related impacts to, and responses of, ecological systems, habitat conditions, and groups of species; these studies include acknowledgement of uncertainty (e.g., Deutsch et al. 2008, Berg et al. 2009, Euskirchen et al. 2009, McKechnie and Wolf 2009, Sinervo et al. 2010, Beaumont et al. 2011, McKelvey et al. 2011, Rogers and Schindler 2011).

Many analyses involve elements that are common to climate change vulnerability assessments. In relation to climate change, vulnerability refers to the degree to which a species (or system) is susceptible to, and unable to cope with, adverse effects of climate change, including climate variability and extremes. Vulnerability is a function of the type, magnitude, and rate of climate change and variation to which a species is exposed, its sensitivity, and its adaptive capacity (IPCC 2007a, Glick et al. 2011). There is no single method for conducting such analyses that applies to all situations (Glick et al. 2011). We use our expert judgment and appropriate analytical approaches to weigh relevant information, including uncertainty, in our consideration of various aspects of climate change.

Global climate projections are informative, and, in some cases, the only or the best scientific information available for us to use. However, projected changes in climate and related impacts can vary substantially across and within different regions of the world (IPCC 2007a). Therefore, we use “downscaled” projections when they are available and have been developed through appropriate scientific procedures, because such projections provide higher resolution information that is more relevant to spatial scales used for analyses of a given species (Glick et al. 2011).

Localized projections suggest the southwestern United States may experience the greatest temperature increase of any area in the lower 48 States (IPCC 2007a), with warming increases in southwestern States greatest in the summer. The IPCC also predicts hot extremes, heat waves, and heavy precipitation will increase in frequency (IPCC 2007a).

An increased risk of drought could occur if evaporation exceeds precipitation levels in a particular region due to increased greenhouse gases in the atmosphere (CH2M HILL 2007). The Edwards Aquifer is also predicted to experience additional stress from climate change that could lead to decreased recharge and low or ceased spring flows given increasing pumping demands

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(Loaiciga et al. 2000). A reduction of recharge to aquifers and a greater likelihood for more extreme droughts were identified as potential impacts to water resources (CH2M HILL 2007). The droughts of 2008–2009 and 2010–2011 were two of the worst short-term droughts in central Texas history, with the period from October 2010 through September 2011 being the driest 12 month period in Texas since rainfall records began (Lower Colorado River Authority (LCRA) 2011). As a result, the effects of climate change could compound the threat of decreased water quantity due to drought.

Edwards Aquifer Modeling and Springflows

Previous analyses associated with the EARIP HCP (HDR Engineering, Inc. et al. 2011) estimated Comal and San Marcos springflows over a 54-year period, including DOR conditions. The analyses relied on modeled springflow regime that included Edwards Aquifer use of 6,714 acre-feet per year in Bexar County by JBSA. On average, in recent years, JBSA has been using about 5,000 acre-feet per year or about 1.2 percent of total Edwards withdrawals. On average, in recent years, National Fish Hatcheries have averaged less than 300 acre-feet per year. Since this modeled Federal pumping rate likely exceeds the current average Federal pumping rate (combined Edwards Aquifer use of JBSA and Service fish hatcheries), we use the EARIP HCP modeled springflows to conservatively assess the effects of the considered action (JBSA Edwards Aquifer use).

4.b. Analysis for effects of the action

4.b.i. Texas wild-rice

Effects of the action on Texas wild-rice

During periods of average precipitation and recharge the effects of JBSA pumping is not expected to appreciably reduce aquifer levels or flow at San Marcos Springs - River. However, during drought, JBSA Edward aquifer groundwater use in part (and overall use in aggregate) will lower aquifer levels and San Marcos springflow. Reduced springflow results in lower than average river flow and certain TWR stands may be damaged (or die) due to inadequate water depth.

The Recovery Plan for TWR states that reduced springflow is the greatest threat to the species (Service 1996a). TWR is intolerant of desiccation, and recent drought events that dewatered portions of the river resulted in the death of stands of the species. Under projected maximum pumping permitted and recent average pumping totals described in the environmental baseline above, San Marcos Springs are anticipated to cease flowing during a repeat of DOR-like conditions. The resulting cessation of flow in the San Marcos River would likely result in the loss of most TWR stands in the San Marcos River. Stands located in Spring Lake or in deeper stretches of the San Marcos River might survive these conditions for an undetermined period of time, but the loss of required dissolved carbon dioxide associated with flowing Edwards Aquifer spring water could adversely affect the species.

JBSA’s aquifer management (reducing withdrawals consistent with regional cutbacks) is

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expected to maintain San Marcos springflows during DOR conditions. While TWR stands are expected to decrease in areal coverage during drought, TWR coverage is expected to grow 5 to 20 percent annually during average flows. JBSA Edwards use is not expected to appreciably reduce the survival and recovery of TWR in the wild.

Effects of the action on designated critical habitat

Designated critical habitat for TWR in Spring Lake and the San Marcos River downstream to its confluence with the Blanco River must provide flowing water of appropriate quality, undisturbed habitats and natural substrates, and minimal physical disturbance to individual plants.

During periods of average precipitation and recharge, JBSA’s Edwards use is not expected to appreciably reduce aquifer levels or San Marcos Springs – River flow. JBSA pumping is not expected to discernibly affect TWR PCE 1 (clear water) or TWR PCE 2 (natural springflow regime). The effect of the action on critical habitat for TWR during average precipitation and recharge conditions are therefore discountable. TWR PCE 3 (constant water temperature) is related to TWR PCE 2 and JBSA pumping is not expected to affect the water temperature regime in the upper San Marcos River. The action has no connection to TWR PCE 4 (maintenance of natural substrate). During drought conditions, the action is expected to slightly reduce springflows at San Marcos Springs. Under Stage V (the most severe drought conditions), JBSA plans to pump from the Edwards Aquifer no more than 502 acre-feet per month (about 8.3 cfs). According to the aquifer modeling presented in the BA (BA Table 9-3), JBSA pumping has on the average a larger effect to Comal Springs than San Marcos Springs. Those simulations indicated that JBSA pumping affects San Marcos Springs by less than 1 cfs. The PCEs for TWR critical habitat are not expected to be adversely affected by JBSA pumping over the next 15 years.

4.b.ii. Peck’s Cave Amphipod

Effects of the action to Peck’s cave amphipod

Peck’s cave amphipod (PCA) occurs at Comal Springs, Hueco Springs, and the Edward aquifer near these springs. During periods of average precipitation and recharge the effects of JBSA pumping is not expected to appreciably reduce aquifer levels or flow at Comal Springs or Hueco Springs. However, during drought, JBSA Edward aquifer use in part (and overall use in aggregate) will slightly lower aquifer levels and slightly reduce Comal Springs flow. The main adverse effects of the proposed action on PCA are anticipated to be the dewatering of PCA habitat in the Spring runs No. 1, 2, and 3 during: (1) moderate drought and (2) severe multiyear drought (DOR like event). In general, we expect dewatering of spring run habitat to: (1) either kill PCA, which would be stranded among exposed gravels and rocks or (2) result in the movement of some PCA (with the opportunity) to stay submerged, going down through the interstices to lower elevations.

The extent of the subterranean range of the Peck’s cave amphipod is unknown. Nearly all specimens collected have been from Comal Springs and areas near spring orifices. The eyeless unpigmented species is generally believed to be associated with subterranean environments and

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habitat near springs. It has been found in drift nets, kick nets, and on cloth lures set at Comal Springs and Hueco Springs. A bottle trap set in Panther Canyon well has caught Peck’s cave amphipods. The presence of PCA at these locations and its lack of vagility (limited ability to move) support the hypothesis that this species may have survived the DOR event by occupying deeper parts of the aquifer.

The various spring outlets in the Comal Springs system are located at different elevations above mean sea level (msl). As aquifer levels fluctuate, flows at a given spring orifice (outlet) depend on its elevation relative to aquifer level. At aquifer levels of about 622 feet msl, Comal Spring runs No. 1 and No. 2 cease to flow and this aquifer level corresponds with Comal springflows of 130 cfs. Thornhill estimated Comal Spring run No. 1 ceases to flow when total Comal Springs discharge is near 100 cfs. Spring run No. 3 ceases flowing at aquifer levels of about 620 to 621 feet msl (LBG – Guyton and Associates 2004), which corresponds to Comal Springs flows of about 50 cfs. EARIP HCP Phase I model runs project that with DOR conditions, flows (monthly mean) in Comal Springs may decline to 27 cfs. It is also uncertain which of Comal Springs at lower elevations will fail during a repeat of DOR conditions. Water levels within Panther Canyon well may continue to provide available habitat for the species. Some Peck’s cave amphipods in Spring runs No. 1, No. 2, and/or No. 3 may be able to reach and use nearby subterranean parts of the aquifer. We estimate the PCA population in Spring runs No. 1, 2 and 3 at 12,462 individuals and the entire PCA population on the surface of Comal Springs and Landa Lake at 33,691 individuals (Table 3). Peck’s cave amphipods unable to remain in or reach suitable habitat may be injured or killed during drought conditions. It is noteworthy that the drought conditions modeled (DOR) are projected to cause total Comal springflow to fall below 130 cfs for a significant period (89 consecutive months, corresponding to the period June 1950 through October 1957, or more than 7 years). For the EARIP HCP biological opinion, we previously estimated the take of PCA associated with a 7-year DOR event at 17,360 PCA individuals.

The EARIP HCP model runs for Phase I and II provide an estimate of Comal Springs flow for a period of about 50 years that includes: (1) DOR-like aquifer recharge sequence, (2) current critical period management, and (3) JBSA pumping. Focusing on the part of the model run after the DOR (1957 and later), there are four periods where Comal Springs flow (monthly mean) is estimated to be 100 cfs or lower (See Figure 4). These non-DOR low flow events appear in the Comal Springs trace for both Phase I and II. While it is unlikely that the next 15 years will have a recharge sequence identical to the one modeled, the model output is useful to roughly understand potential habitat losses and incidental take of PCA. We anticipate that non-DOR low flow events (where monthly mean Comal Springflow is 100 cfs or less) will occur once or twice over the next 15 years. The modeling indicated four events in about 40 years and we infer there will be a low flow event once over the next 15 years. During one of these non-DOR low flow events, we estimate half of the PCA present in Comal Spring runs No. 1, 2, and 3 will die among the dewatered habitat (See Table 4). We estimate the take of PCA from low flows other than a DOR event will be 6,231 PCA, driven by a reduction in (half) the carrying capacity. Table 5 provides an accounting of PCA take in general due to low flows and the PCA take at Comal Springs attributable to the action. We estimate the total incidental take of PCA at Comal Springs attributable to JBSA pumping is 283, which is 1.2 percent of PCA incidental take resulting from one DOR event and one non-DOR low flow event.

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The various spring outlets at Hueco Springs have reportedly ceased flowing under various drought conditions. The effect of the action, however, is expected to generate increases in aquifer levels that may provide some support for continued springflows at Hueco Springs, though no data is available to assess the certainty and magnitude of this potential effect. The persistence of the species at this location despite the multiple recorded incidences of drought- induced cessation of flow further supports suggestions that the species relies primarily on the subterranean aquatic habitats rather than the surface expressions of the Edwards Aquifer.

Peck’s cave amphipod is believed to occupy subterranean areas within the aquifer and wetted habitats near spring openings though no abundance or density data are available to resolve where (particularly in the vertical axis) most of the extant Peck’s cave amphipods occur. Calculating the amount of potential take based on surface effects (such as drying of surface spring openings) to estimated surface populations, therefore, generates a total that likely overestimates the overall effects to the species. This factor provides some measure of conservatism in the calculations. We estimate a total surface population of Peck’s cave amphipods in the Comal Springs system at 21,700 based on sampling data reported to the Service (Bowles and Stanford 2003, Gibson et al 2008). No estimate is available for the population associated with Hueco Springs or the Edwards Aquifer near Hueco Springs.

Drying of surface habitat and spring orifices may affect the species and the availability of its required food resources in these areas during a repeat of DOR conditions.

The spring outlets near the western shoreline of Landa Lake and the upwellings near Spring Island are expected to decline but to continue to provide flow supporting the needs of the species at these locations. Approximately 80 percent of the estimated surface populations of Peck’s cave amphipods are associated with Comal Spring runs No. 1, No. 2 and No. 3, and these individuals will be subject to displacement, injury or death during these conditions. According to the biological opinion for the EARIP HCP, about 17,360 Peck’s cave amphipods will be subject to take during a repeat of DOR-like conditions in the Comal Springs system.

The impact of the taking during DOR conditions, therefore, could impact Peck’s cave amphipods at Comal Springs. We believe evidence suggests that the species successfully relied on subsurface habitats in the past to survive drought conditions, and that the species’ persistence at Comal Springs following the DOR event supports this hypothesis. Because the effects of the action will maintain habitat conditions surpassing those experienced during the DOR, and while the effects of the taking at Comal Springs may have some population-level effects in the short term, we believe that the species is capable of surviving and repopulating these locations after an event of similar duration and intensity.

The total number of Peck’s cave amphipods affected by JBSA pumping during a repeat of a seven-year DOR event is uncertain. The BA indicates that JBSA pumping affects total Comal Springs flow on average by less than 7 cfs. The species apparently survived the seven-year DOR event. If higher elevation springs of Comal Springs fail, Peck’s cave amphipods may be able to persist in nearby subterranean aquatic habitats within the aquifer (for example, in gravel-filled fissures with some groundwater flow). The effects of JBSA pumping that result in take of Peck’s cave amphipod is not expected to appreciably reduce the likelihood of survival and

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recovery of the species in the wild.

Effects of the action on designated critical habitat

Critical habitat for the species was designated in two units located at Comal Springs and Hueco Springs (72 FR 39248).

The effects of the action are to slightly decrease flow at Comal Springs during (1) a drought of record event (DOR) and (2) a non-DOR low flow event. The duration of a DOR event is about five years and the duration of the non-DOR low flow event is about one month. Aquifer modeling has not focused on estimating Hueco Springs flow. The effects of JBSA pumping on Hueco Springs flow and the Hueco Springs critical habitat unit are uncertain. Though Comal Springs flow may be slightly decreased by the action, it will not affect designated critical habitat from continuing to provide PCA PCE 1 (high-quality water). PCA PCE 2 (aquifer water temperature) and PCA PCE 3 (food supply) are expected to be maintained as JBSA pumping reductions are matched by regional aquifer management measures.

The effects of the action will not destroy or adversely modify the ability of the designated critical habitat of the Peck’s cave amphipod to provide the identified primary constituent elements required for the conservation of the species.

4.b.iii. Comal Springs dryopid beetle

Effects of the action on the Comal Springs dryopid beetle

Comal Springs dryopid beetle (CSDB) occurs at Comal Springs, Fern Bank Springs, and the Edward aquifer near these springs. During periods of average precipitation and recharge the effects of JBSA pumping is not expected to appreciably reduce aquifer levels or flow at Comal Springs. JBSA pumping is not expected to affect Fern Bank Springs flow or CSDB that may occur there. However, during drought, JBSA Edward aquifer use in part (and overall use in aggregate) will slightly lower aquifer levels and slightly reduce Comal Springs flow.

Reduction or loss of water has been described as one of the main threats to the Comal Springs dryopid beetle. Most of the CSDB collected to date have been found in the Comal Spring runs No. 1, 2, and 3. During DOR conditions, Comal Springs spring runs No. 1, 2, and 3 are expected to fail. For the EARIP HCP biological opinion, we have previously estimated the take of CSDB associated with a 7-year DOR event at 1,471 CSDB individuals. Based on HDR Engineering Inc. et al. (2011 modeling), during low flow conditions other than a DOR event, Comal Springs spring runs No. 1, 2, and 3 are anticipated to fail (for about a month) once in the next 15 years (Figure 4). During one of these non-DOR low flow events, we estimate half of the CSDB present in Comal Spring runs No. 1, 2, and 3 will die among the dewatered habitat. We estimate the take of CSDB at Comal Springs (surface) due to a low flows other than a DOR event will be 729 CSDB. This type of low flow event is expected to be in the 60 to 100 cfs range lasting about 1 month. Table 5 provides an accounting of CSDB take in general due to low flows and CSDB take at Comal Springs attributable to the action. We estimate the total incidental take of CSDB at Comal Springs attributable to JBSA pumping is 26, which is 1.2 percent of CSDB incidental

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take resulting from one DOR event and one non-DOR low flow event.

The Comal Springs dryopid beetle’s specialized subterranean and aquatic adaptations limit the species’ ability to utilize new habitats or expand its range. CSDB cannot swim or fly, and it has been suggested that they may be confined to small areas surrounding spring openings. The extent of the subterranean range of the species is unknown, though to date it is only known from natural spring openings at Comal Springs and Fern Bank Springs and from a bottle trap set in Panther Canyon well. CSDB may have survived the DOR event by utilizing subterranean components of the aquifer and springs systems. However, no information is available on the CSDB distribution or population trends during the DOR.

The various spring outlets in the Comal Springs system are located at different elevations. As aquifer levels fluctuate, flows at a given spring orifice (outlet) depend on its elevation relative to aquifer level. At aquifer levels of about 622 feet msl, Comal Spring runs No. 1 and No. 2 cease to flow and this aquifer level corresponds with Comal springflows of 130 cfs. The EARIP HCP (2012)(Chapter 3.1.5.4, Effects of the Drought of Record on Comal Springs) discusses the total Comal Springs flow values and Landa Park well water levels that correspond to flows stopping in Spring runs No. 1, No. 2, and No. 3. That discussion is based primarily on the review by LBG – Guyton and Associates (2004). Spring run No. 3 ceases flowing at aquifer levels of about 620 to 621 feet msl (LBG – Guyton and Associates 2004), which corresponds to Comal Springs flows of about 50 cfs . For the next 8 years (EARIP HCP Phase I), modeling projects that with DOR conditions, flows (monthly mean) in Comal Springs may decline to 27 cfs. Under these conditions, flows will fail at Comal Spring runs No. 1, No. 2, and No. 3. It is uncertain which of the Comal Springs are fully or partially associated with the upthrown block. It is also uncertain which of Comal Springs at lower elevations will fail during a repeat of DOR conditions. Water levels within Panther Canyon well may continue to provide available habitat for this species. Some Comal Springs dryopid beetles in Spring runs No. 1, No. 2, and/or No. 3 may be able to reach and use nearby subterranean parts of the aquifer. Those unable to reach suitable habitat may be injured or killed during drought conditions as spring run habitat is dewatered.

The hydrology supporting Fern Bank Springs is not sufficiently understood to predict how pumping in Bexar County may impact flows at Fern Bank Springs. As discussed above, Fern Bank may be somewhat disjunct from the part of the Edwards Aquifer supplying Comal and San Marcos springs. Fern Bank Springs may be partially sourced from the Edwards Aquifer to the south of Fern Bank Springs. Though this spring system has been described as never ceasing to flow, there is no data available to either support or refute that claim.

The Comal Springs dryopid beetle is believed to occupy subterranean areas within the aquifer as well as wetted habitats near Comal and Fern Bank springs. The species is also known from Comal Springs spring runs, upwellings and springs that occur some distance from shoreline, and from Panther Canyon well. Calculating the amount of potential take based on surface effects (such as drying of surface spring openings) to the CSDB surface populations is uncertain as we do not know how many individuals will be able to move to lower elevations where suitable habitat may remain. We estimate a total surface population of Comal springs dryopid beetles in the Comal Springs system at 1,839 individuals (Bowles et al. 2003, Gibson 2011). No estimate is available for the population associated with Fern Bank Springs or subterranean habitats of the

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Edwards Aquifer.

Drying of surface habitat and spring orifices may affect the species and the availability of its required food resources during a repeat of DOR conditions. The potential drying of Comal Springs runs No. 1, No. 2, and No. 3 during DOR conditions will result in displacement, injury, or death of an unknown number of Comal Springs dryopid beetles.

The total number of Comal Springs dryopid beetles displace, harmed, or killed by JBSA pumping is uncertain. Because the species apparently survived the seven-year DOR event, and is believed to occur primarily in subterranean aquatic habitats within the aquifer, we believe that this level of take resulting from JBSA use of the Edwards Aquifer will not appreciably reduce the likelihood of survival and recovery of the species in the wild.

Effects of the action on designated critical habitat

Critical habitat for the species was designated in two units located at Comal Springs and Fern Bank Springs (72 FR 39248).

One effect of the action is to slightly decrease flow at Comal Springs during a drought of record event and other low flow periods. The effect of JBSA pumping on Fern Bank Springs flow and CSDB habitat is considered discountable as we have no information that links Fern Bank Springs to the Edwards Aquifer regional flowpaths from Bexar and Comal counties.

Though Comal Springs flow may be slightly decreased by the action, it will not affect designated critical habitat from continuing to provide CSDB PCE 1 (high-quality water). PCA PCE 2 (aquifer water temperature), CSDB PCE 3 (springflows providing adequate dissolved oxygen), and CSDB PCE 4 (food supply) are expected to be maintained as JBSA pumping reductions are matched by regional aquifer management measures.

The effects of the action will not destroy or adversely modify the ability of the designated critical habitat of the Comal Springs dryopid beetle to provide the identified primary constituent elements required for the conservation of the species.

The effect of the action is not expected to: (1) pose any water quality issues, (2) increase pollutants, or (3) affect springflow temperatures in either of the CSDB critical habitat units.

JBSA activities including Edwards pumping are not expected to destroy or adversely modify the ability of designated Comal Springs dryopid beetle critical habitat from providing the four identified primary constituent elements required for the conservation of the species.

4.b.iv. Comal Springs riffle beetle

Effects of the action on the Comal Springs riffle beetle

Comal Springs riffle beetle (CSRB) occurs at Comal Springs, San Marcos Springs, and the Edward aquifer near these springs. During periods of average precipitation and recharge, the

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effects of JBSA pumping are not expected to appreciably reduce aquifer levels or flow at either Comal Springs or San Marcos Springs. JBSA pumping is not expected to appreciably affect San Marcos Springs or CSRB that may occur there. However, during drought, JBSA Edward aquifer use in part (and overall use in aggregate) will slightly lower aquifer levels and slightly reduce Comal Springs flow.

Reduction or loss of water has been described as one of the main threats to the CSRB. Most of the CSRB collected to date have been found in the Comal Spring runs No. 1, 2, and 3. During drought conditions (Comal Springs flow in the 130 to 50 cfs range), Comal Springs spring runs No. 1, 2, and 3 are expected to fail.

Comal Springs System

For the EARIP HCP biological opinion, we have previously estimated the take of CSRB associated with a 7-year DOR event (15,451 CSRB). Based on HDR Engineering Inc. et al. (2011 modeling), during low flow conditions other than a DOR event, Comal Springs spring runs No. 1, 2, and 3 are anticipated to fail (for about a month) once in the next 15 years (Figure 4). During one of these non-DOR low flow events, we estimate half of the CSRB present in Comal Spring runs No. 1, 2, and 3 will die among the dewatered habitat. We estimate the take of CSRB at Comal Springs (surface) due to a low flows other than a DOR event will be 3,596 CSRB. This type of low flow event is expected to be in the 60 to 100 cfs range lasting about 1 month. Table 5 provides an accounting of CSRB take in general due to low flows and CSRB take at Comal Springs attributable to the action. We estimate the total incidental take of CSRB at Comal Springs attributable to JBSA pumping is 172, which is 1.2 percent of CSRB incidental take resulting from one DOR event and one non-DOR low flow event.

San Marcos Springs System

We are uncertain about the effects of the proposed action on CSRB habitat in Spring Lake. The effect of the action at San Marcos Springs is expected to be attenuated relative to its effect at Comal Springs. The EARIP HCP models for San Marcos springflow indicate that EARIP HCP Phase I management will maintain average monthly flows above 50 cfs.

The CSRB has limited vagility. The aquatic species cannot fly, and it has been suggested that they may be confined to small areas surrounding spring openings. The extent of the subterranean range of the species is unknown, though to date it is only known from natural spring openings at Comal and San Marcos Springs.

Drying of surface habitat and spring orifices may affect the species and the availability of its required food resources in these areas during a repeat of DOR conditions. About 90 percent of the CSRB habitats known to be occupied in the Comal Springs system are associated with the primary spring outlets.

An unknown number of CSRBs in the Comal Springs system would be harmed, displaced, or killed during DOR conditions. As stated above, a repeat of the DOR would result in an extended loss of flow in Comal Springs Spring runs No. 1, 2, and 3. The impact of the taking during DOR

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conditions, therefore, may adversely impact the population at Comal Springs. The species appears to have survived in subsurface habitats in the past to survive drought conditions.

CSRBs in Spring Lake are expected to survive DOR conditions, as the minimum continuous flows of 50 cfs are similar to those reported during the DOR which the species apparently survived in this location. Though some incidental take associated with the action may occur during these conditions in Spring Lake, the effects of the taking are not expected to exert a demographic or population-level effect on the population at this location under these conditions due primarily to the slight effect JBSA pumping is expected to have on San Marcos Springs flow.

The CSRB displays overlapping generations, is apparently capable of multiple broods per season, and reportedly lives for six months to three years. We anticipate that the adverse effects to the Comal population from JBSA pumping will not appreciably affect the survival of the species in the Comal Springs system.

Effects of the action on designated critical habitat

Critical habitat for the species was designated in two units located at Comal Springs and San Marcos Springs (72 FR 39248). While higher elevation parts of the Comal Springs unit will (under DOR conditions) have an altered hydrologic regime (CSRB PCE 3), lower elevation springs are projected to maintain some springflow and support basic biological functions of CSRB PCE 1, 2, 3, 4, and 5). During DOR conditions, parts of the Comal Springs unit are anticipated to continue to provide the PCE need for conservation of the species. The effects of JBSA pumping is not expected to destroy or adversely modify the ability of the proposed designated critical habitat of the CSRB from providing the identified primary constituent elements required for the conservation of the species. The San Marcos unit is expected to maintain all CSRB PCE even during a DOR event that is predicted to decrease San Marcos springflow to 50 cfs (monthly mean).

4.b.v. San Marcos Gambusia

Effects of the action on the San Marcos gambusia

The SMG has not been collected since 1982, and may no longer exist in the wild. The species has not, however, been declared extinct or removed from the list of endangered species and must therefore be addressed in this biological opinion. The effect of JBSA pumping on San Marcos Springs flow, on the average, is estimated to be less than 1 cfs. Multiple efforts to find this species in the San Marcos River have failed. The drought related reductions in JBSA pumping matched by Edwards Aquifer users region-wide is expected to maintain San Marcos Springs – River flow above 50 cfs even in DOR conditions.

Effects of the action on designated critical habitat

The designated critical habitat for the species includes the San Marcos River from Highway 12

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Bridge downstream to approximately 0.5 miles (0.8 km) below Interstate Highway 35 Bridge (45 FR 47355).

JBSA pumping is not expected to alter the function of any of the SMG critical habitat PCE. The action is not expected to discernibly affect: SMG PCE 1 (open areas with low water velocities and little aquatic vegetation), SMG PCE 2 (natural substrates), or water temperatures of the upper San Marcos River (SMG PCE 3). The effects of the action will not appreciably reduce the ability of designated critical habitat to support SMG.

4.b.vi. Fountain darter

Effects of the action on the fountain darter

JBSA’s Edwards Aquifer withdrawals affect the fountain darter by slightly reducing flows at Comal and San Marcos springs. During periods of average precipitation and recharge, the effects of JBSA groundwater use on fountain darters will be difficult to discern in these spring systems.

Reduced springflow is considered one of the primary threats to the fountain darter. During periods of drought, a small reduction in flows at Comal or San Marcos springs would be expected to decrease fountain darter habitat suitability, particularly in downstream reaches. The effects of the action, therefore, during droughts, would slightly decrease the carrying capacity of the Comal and upper San Marcos rivers for fountain darters.

The loss of water quality is also identified as a primary threat to the fountain darter. The effects of the action during drought include an increase in turbidity and water temperatures in summer months. Lower springflows: (1) increase retention time in the Comal and San Marcos rivers, (2) increase areas accessible to water recreationists, and (3) increase water temperatures in summer. For spring adapted ecosystems, increased water temperatures adversely affect the quantity and quality of habitat for aquatic plants, aquatic macroinvertebrates, and fish species.

During DOR conditions, flows at Comal Springs are predicted to decline to 27 cfs for a limited period. Hardy (2010) stated that flows of 30 cfs (with 20 cfs directed down the Old Channel and 10 cfs directed through the new channel) for no more than six-months to be followed by at least three-months of flows of 80 cfs would support juvenile and adult fountain darters and maintain some limited fountain darter recruitment. During DOR conditions, the fountain darter could experience population losses estimated to range between 50 to 94 percent in the San Marcos River system. The fountain darter survived the DOR in Spring Lake and the San Marcos River, and the effects of the action include flow protection and springflow management measures that mimic historic conditions. Fountain darters in Spring Lake are therefore expected to survive a repeat of DOR conditions. Modelers estimate 50 cfs is the lowest discharge (monthly mean) under DOR conditions at San Marcos Springs. Though some decline in the fountain darters of Spring Lake may be associated with these conditions, the specific effect of JBSA pumping on the San Marcos fountain darter population is not expected to be discernible as total flows would be reduced by about 1 cfs. Simulated San Marcos Springs discharge after the modeled DOR event remains above 82 cfs (monthly mean). During low flow conditions at Comal and San Marcos

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springs (not associated with a DOR event), total weighted usable area (WUA) is expected to decline as physical habitat attributes shift in to lower suitability (Institute for Natural System Engineering 2004). Stream water temperatures during low flows in summer is expected to lower fountain darter reproduction (Bonner et al. 1998) The carrying capacity is also expected to decrease as aquatic plant coverage decreases.

Based on HDR Engineering Inc. et al. (2011 modeling), during low flow conditions other than a DOR event, Comal Springs spring runs No. 1, 2, and 3 are anticipated to fail (for about a month) once in the next 15 years (Figure 4). During one of these non-DOR low flow events, we estimate 25 percent of the fountain darters present in Comal and San Marcos springs systems will die among the degraded habitat. We estimate the take of fountain darters at Comal Springs system (including the Landa Lake and Comal River) due to a low flows other than a DOR event will be 193,500 fountain darters. We estimate the take of fountain darters in the San Marcos Springs system (including Spring Lake and the San Marcos River upstream of the Blanco River) due to low flows other than a DOR event will be 223,500 fountain darters. This type of low flow event is expected to be in the 60 to 100 cfs range lasting about 1 month. Table 5 provides an accounting of fountain darter take in general due to low flows and fountain darter take for both Comal and San Marcos rivers attributable to the action. We estimate the total incidental take of fountain darters in the Comal River attributable to JBSA pumping is 11,142, which is 1.2 percent of Comal system fountain darter incidental take resulting from one DOR event and one non- DOR low flow event. We estimate the total incidental take of fountain darters in the upper San Marcos River attributable to JBSA pumping is 8,082, which is 1.2 percent of San Marcos system fountain darter incidental take resulting from one DOR event and one non-DOR low flow event.

The total incidental take of fountain darters for JBSA pumping is 19,224. The total number of fountain darters subject to incidental take as a result of JBSA pumping (assuming a repeat of DOR conditions and one non-DOR low flow event), like other incidental take determinations herein, depends on weather conditions and other factors that are difficult to predict over the next 15 years. Of fountain darters harmed, displaced or killed, we anticipate the effect of JBSA pumping on fountain darters to primarily occur in the Comal Springs system. Fountain darter recruitment, even during drought, is expected to maintain the populations in Landa Lake, the old and new channels and Comal River proper. We believe that the impacts of the taking resulting from JBSA pumping will not appreciably reduce the likelihood of survival and recovery of the species in the wild.

Effects of the action on designated critical habitat

Critical habitat for the fountain darter includes Spring Lake and the San Marcos River downstream to 0.5 mile (0.8 kilometers) past Interstate 35 (45 FR 47355).

The action results in implementation of the flow protection and springflow management measures described above. During drought conditions the combined effects of these measures will maintain springflows at San Marcos Springs, thereby maintaining this required element of designated critical habitat.

The effect of JBSA pumping is not anticipated to appreciably reduce flow in the San Marcos

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system. The action is not likely to affect any of the six identified fountain darter PCE in the San Marcos system and the action will not result in the destruction or adverse modification of the habitats or natural substrates required for the conservation of the fountain darter.

4.b.vii. San Marcos salamander

Effects of the action on the San Marcos salamander

During periods of average precipitation and recharge the effects of JBSA pumping is not expected to appreciably reduce aquifer levels or flow at San Marcos Springs. However, during drought, JBSA Edward aquifer use in part will slightly lower aquifer levels and San Marcos springflow. The modeled effect of JBSA pumping on San Marcos springflow is estimated to be less than 1 cfs. Reduced springflow results in lower than average water surface levels at Spring Lake and potentially inadequate flow over one or both of the Spring Lake Dam spillways.

Reduced springflow is considered one of the primary threats to the SMS. The SMS is also threatened by the potential loss of water quality at San Marcos Springs. The effects of the action are not anticipated to discernibly affect springflow or water quality at San Marcos Springs.

The Edwards HCP projected that during a repeat of DOR conditions, the SMS could experience population losses near the eastern spillway below Spring Lake dam and some of the normally spring-dominated parts of Spring Lake. The Service estimated the number of SMS expected to be harmed or killed during DOR conditions at 233,361. JBSA pumping may be considered to contribute to (result in incidental take of) 1.2 percent of that number or 2,800. The total number of SMS subject to incidental take during a low flow non-DOR conditions is estimated at a loss of 25 percent of individuals or 91,438. SMS incidental take from a low flow non-DOR event attributable to JBSA pumping is 1.2 percent of 91,438 or 1,097.

We estimate the total incidental take of SMS in Spring Lake and nearby areas downstream attributable to JBSA pumping is 3,898 (the difference of 1 individual is due to rounding), which is 1.2 percent of San Marcos system SMS incidental take resulting from one DOR event and one non-DOR low flow event.

The SMS survived the DOR in Spring Lake and nearby parts of the San Marcos River. However, we have no information on SMS abundance before or after the DOR. The effects of the action, JBSA pumping, is not expected to reduce the likelihood of survival and recovery of the species in the wild.

Effects of the action on designated critical habitat

Designated critical habitat for the species consists of Spring Lake and the uppermost approximately 164 feet (50 meters) of the San Marcos River below Spring Lake dam (45 FR 47362).

During periods of average precipitation and recharge the effects of JBSA pumping is not expected to appreciably reduce aquifer levels or flow at San Marcos Springs. However, during

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drought, JBSA Edward aquifer use in part will slightly lower aquifer levels and San Marcos springflow. The modeled effect of JBSA pumping on San Marcos springflow is estimated to be less than 1 cfs. Reduced springflow results in lower than average water surface levels at Spring Lake and potentially inadequate flow over one or both of the Spring Lake Dam spillways.

The effects of the action, JBSA pumping, is not anticipated to discernibly alter SMS PCE 1 (thermally constant water), SMS PCE 2 (flowing water), or SMS PCE3 (clean and clear water). JBSA pumping is anticipated to have no effect on SMS PCE 4 (natural substrates) or SMS PCE 2 (presence of aquatic plants and rocks for cover). The action will not result in the destruction or adverse modification of the habitats or natural substrates required for the conservation of the SMS.

4.b.viii. Texas blind salamander

Effects of the action on the Texas blind salamander

The Texas blind salamander occurs in: (1) the Edwards Aquifer in the San Marcos area, (2) near certain San Marcos Spring orifices, (3) water-filled caves found both north and south of San Marcos Springs, and (4) a small spring associated with Sessoms Creek. TBS are found in water wells completed in the Edwards Aquifer in the San Marcos area. During periods of average precipitation and recharge the effects of JBSA pumping is not expected to appreciably affect Edwards Aquifer flowpaths, Edwards Aquifer levels, or flow at San Marcos Springs. However, during drought, JBSA Edward aquifer use in part will slightly lower aquifer levels and San Marcos springflow. The modeled effect of JBSA pumping on San Marcos springflow is estimated to be less than 1 cfs.

Decreased aquifer levels and loss of springflow are among the threats to the TBS identified in the species’ recovery plan (Service 1996a). The TBS is also threatened by the potential loss of water quality. Because few data are available for estimating population size of the TBS, habitat impacts are relied on to estimate effects to the species that could constitute take.

The effects of the proposed action are not anticipated to affect aquifer levels and springflows to the point that we would be able to discern harm or death of TBS. Some habitat in recharge zone caves and near spring orifices may be slightly affected in terms of availability during a repeat of DOR conditions. Under existing baseline conditions, aquifer levels are not expected to drop to a level that would result in cessation of flow at San Marcos Springs as the EARIP HCP measures are expected to maintain San Marcos springflow at or above 50 cfs. Because the species is believed to have survived the seven-year DOR event, and the effects of the action will maintain springflows at levels that mimic those historic conditions, we find that effects of the incidental taking resulting from JBSA pumping will not appreciably reduce the likelihood of survival and recovery of the species in the wild.

Effects of the action on designated critical habitat

Critical habitat has not been designated for the TBS; therefore, none will be impacted by the action.

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5. Cumulative Effects

Cumulative effects include the effects of future State, local, or private actions that are reasonably certain to occur in the action area considered in this biological opinion. Future Federal actions that are unrelated to the action are not considered in this section because they require separate consultation pursuant to section 7 of the Act.

The action area includes 17 counties and the duration of the proposed permit is 15-years. Because of this broad spatial extent and extended duration, exact identification of all present and reasonably foreseeable future activities is not feasible. However, identification of generalized activities and their impacts is possible and can be used to analyze their cumulative effect. Therefore, the cumulative impacts assessment is not project specific or quantifiable, but provides an overview of present and reasonably foreseeable projects.

Transportation projects currently planned or under construction in the action area could generate effects in addition to those expected under the action. Locally funded non-Federal transportation projects such as county or municipal road projects could occur within the action area during the duration of the proposed permit. It is beyond the scope of this evaluation to analyze each of these transportation projects on an individual basis, but the effects of transportation projects are considered as for their potential to generate effects cumulative to the action.

Transportation projects over the contributing and recharge zones of the Edwards Aquifer could impact aquifer recharge and thereby affect springflow. While the overall area affected by these projects represent a small percentage of the total action area, individual recharge sites that contribute significant recharge capacity can be affected by relatively small changes in surface contours, impervious surfaces, or vegetative cover. Alterations to recharge capacity or function could reduce inflows into the Edwards Aquifer and adversely impact springflows. The cumulative effects of reduced recharge capacity could result in further negative effects to springflows. Careful project design that identifies and avoids or provides adequate buffer zones around such recharge features throughout the study area can minimize the effects of these impacts.

Water infrastructure projects may have beneficial cumulative effects to Edwards Aquifer springflows. Projects that result in diversified water supplies or reduced demand for Edwards Aquifer water near Comal and San Marcos Springs may allow for increased aquifer levels that would support springflows. Recharge enhancement structures within the contributing zone have been proposed to store surface water runoff for later release into the recharge zone. Proposed reservoirs within the recharge zone would impound surface water runoff to directly recharge the Edwards Aquifer. During periods of normal or high precipitation, these structures could provide some additional recharge that would support the aquifer-fed springs. Such structures would only be expected to provide these benefits, however, when adequate precipitation provides surface flows to be impounded and stored for these uses. During DOR-like conditions, these structures are anticipated to be of little value to Edwards Aquifer recharge or springflow, and would be expected to have little cumulative effect to the considered action.

Reasonably foreseeable private and public land development activities could adversely affect

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springflows through various actions. Development that negatively affects recharge features through actions such as alteration of land contours or increasing impervious cover can result in reduced Edwards Aquifer inflows in much the same way as transportation projects. Development projects that generate additional demand for Edwards Aquifer water could reduce water volumes available for springflow.

Some natural resource management actions within the study area could provide cumulative effects benefitting springflows. Some reasonably foreseeable projects seek to ensure that recharge features continue to provide Edwards Aquifer inflows through voluntary conservation efforts or by way of municipal, county, or State-mandated regulatory measures. The efforts of non-governmental organizations (NGOs) such as the Bexar Land Trust, the Nature Conservancy, Texas Cave Management Association, and the Trust for Public Land, among others, to acquire or put legal mechanisms in place to conserve lands over the recharge and contributing zones have and are expected to continue to contribute to Edwards Aquifer recharge and springflows. Regulatory approaches such as existing City of San Antonio impervious cover limitations and TCEQ regulations regarding activities over the Edwards Aquifer further protect recharge and enhance springflows. Public education and outreach programs such as those employed by SAWS and the EAA that reduce demand for pumped Edwards Aquifer water also support increased springflows, though by an unquantifiable amount.

Reasonably foreseeable water quality within the study area is associated with population growth and effects may result from current or future actions within the study area. Projected population growth throughout the region is expected to result in greater urbanization and includes ongoing or planned transportation, water supply, and other development projects that may affect water quality. Urban and suburban development can increase the risk of water quality degradation associated with point and non-point source pollution.

Some groundwater quality effects are the result of reasonably foreseeable transportation, water supply, and land development actions. Existing and ongoing development in some San Antonio, New Braunfels and San Marcos watersheds have the potential to directly affect the quality of recharge waters that could impact groundwater by increasing impervious cover, stormwater runoff, and other non-point source impacts associated with increasing development density. Ongoing and future development associated with projected population growth could be reasonably expected to contribute to additional water quality impacts.

On June 14, 1992, the Edwards Aquifer levels reached a historic high level of 703.3 feet (above mean sea level (msl) or NGVD 1929) at the Bexar Index Well (J-17). However, in about four years (August,1996), springflows declined to the 83 cfs in the Comal system and 76 cfs in the San Marcos system. This illustrates that the aquifer can effectively be full and springflow discharge rates may significantly decline in a matter of four years, even when annual mean recharge (1993-1996) is 460,350 acre-feet.

Additionally other local threats are likely to continue to occur, some of which will be exacerbated by low flows, further reducing the chances of conservation and recovery of the species.

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6. Biological Opinion Conclusion

After reviewing the current status, the environmental baseline, the effects of the proposed action and the cumulative effects, it is the Service’s biological opinion that the action, as proposed, is: (1) not likely to jeopardize the continued existence of Texas wild-rice, Peck’s cave amphipod, Comal Springs dryopid beetle, Comal Springs riffle beetle, San Marcos gambusia, fountain darter, San Marcos salamander, or Texas blind salamander; and (2) is not likely to destroy or adversely modify designated critical habitat for Texas wild-rice, Peck’s cave amphipod, Comal Springs dryopid beetle, Comal Springs dryopid beetle, San Marcos gambusia, fountain darter, or San Marcos salamander.

The effect of the proposed action on these species and their respective critical habitat is summarized below. The changes in flow caused by the proposed action at Comal and San Marcos springs are presented in the BA (BA Table 9-3). These modified flows, in part, provide the basis for understanding the extent of adverse effects on these two spring systems. Only limited inferences can be made about the effect of the proposed action on flow at Hueco Springs. As discussed above, a groundwater divide has been hypothesized to occur between Fern Bank and San Marcos springs and we do not anticipate the proposed action to affect Fern Bank Springs, the Comal Spring dryopid beetle at Fern Bank Springs, or the CSDB critical habitat unit at Fern Bank Springs.

Texas wild-rice depends on San Marcos springflows (long-term average discharge is 174 cfs). The proposed action is anticipated to have a small effect on San Marcos Springs discharge. The decrease in San Marcos springflow attributable to JBSA pumping is less than 2 cfs. Even during drought, the effect of water pumped for the JBSA on San Marcos River instream flow is not likely to result in loss of Texas wild-rice stands. The small project- related decrease in San Marcos River (about 2 percent) is not likely to adversely modify Texas wild-rice critical habitat.

Peck’s cave amphipods depend on flow through the Edwards Aquifer and spring habitat at Hueco and Comal springs. The largest PCA population is likely associated with Comal Springs and nearby parts of the Edwards Aquifer. The proposed action is anticipated to have a small effect on Comal Springs discharge. While some of Comal Springs (long-term average total springflow about 290 cfs) are anticipated to temporarily stop flowing over the next 15 years, JBSA pumping is not expected to affect a significant portion of Comal Springs discharge. The proposed action is anticipated to affect less than 2 percent of the Comal Springs PCA population. Project-related decrease in Comal Springs flow is not likely to adversely modify PCA critical habitat.

Comal Springs dryopid beetles depend on flow through the Edwards Aquifer and spring habitat at Comal Springs and Fern Bank Springs. The largest CSDB population is likely associated with Comal Springs and nearby parts of the Edwards Aquifer. The proposed action is anticipated to have a small effect on Comal Springs discharge. While some of Comal Springs (long-term average total springflow about 290 cfs) are anticipated to temporarily stop flowing over the next 15 years, JBSA pumping is not expected to affect a significant portion of Comal Springs discharge or CSDB habitat. The proposed action is anticipated to affect less than 2 percent of the Comal Springs CSDB population. Project-related decrease in Comal Springs flow is not likely to

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adversely modify CSDB critical habitat. Fern Banks Springs was discussed at the beginning of this section and the proposed action is not likely to adversely modify the CSDB critical habitat at Fern Bank Springs.

Comal Springs riffle beetles depend on Comal and San Marcos springflow. The largest CSRB population is likely associated with Comal Springs. The proposed action is anticipated to have a small effect on Comal Springs discharge. While some of Comal Springs (long-term average total springflow about 290 cfs) are anticipated to temporarily stop flowing over the next 15 years, JBSA pumping is not expected to affect a significant portion of Comal Springs discharge or CSRB habitat. The proposed action is anticipated to affect less than 2 percent of the Comal Springs CSRB population. The small project-related decrease in Comal Springs flow is not likely to adversely modify CSRB critical habitat.

San Marcos gambusia, if extant, requires adequate instream flow in the San Marcos River. The proposed action is anticipated to have a small effect on San Marcos Springs discharge. The decrease in San Marcos springflow attributable to JBSA pumping is less than 2 cfs. Even during drought, JBSA pumping’s effect on San Marcos River instream flow is not likely to result in loss of San Marcos gambusia habitat and is not likely to adversely modify San Marcos gambusia critical habitat.

The fountain darter depends on adequate Comal and San Marcos springflow (long-term average 290 and 174 cfs respectively). The proposed action is expected to decrease flow at Comal and San Marcos by less than 10 and 2 cfs respectively. One of the main effects of decrease springflow is an increase in summertime water temperatures and a decrease in fountain darter reproduction. Thermal refugia are expected to persist in both the Comal and San Marcos rivers even during a drought. A suitable water temperature regime (for fountain darter reproduction) is anticipated to follow low flow events and fountain darters are expected to recolonize previously occupied reaches of the Comal and upper San Marcos rivers. The project-related effects on fountain darters in these rivers are not expected to reach the level that affects population viability.

The San Marcos salamander depends on San Marcos springflow and the proposed action is expected to affect springflow by less than 2 cfs (or about 1 percent of the long-term average). Spring Lake is fed by springs at various elevations and San Marcos salamanders in the lake are not anticipated to be affected by this slight change in springflow. The population size of San Marcos salamanders in Spring Lake and nearby areas downstream is estimated at 365,750 individuals. The estimated project-related take of San Marcos salamanders (3,898 individuals) accounts for the drought of record and a low flow event (San Marcos Springs monthly mean 80 to 85 cfs) other than the drought of record.

The TBS depends on the flow and water quality of the Edwards Aquifer in the San Marcos area. The project–related effects to this part of the Edwards Aquifer are not expected to result in the death of any TBS. During a drought of record, Edwards Aquifer levels may fall to unprecedented levels though EARIP HCP measures are expected to maintain levels supportive of TBS. The TBS is known from several caves (Ezells and Rattlesnake caves) where there appears to be no barrier to moving to lower elevations. The project-related effects to the TBS and its

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habitats are expected to be small (e.g., decrease of San Marcos springflow by 2 cfs) and we find that JBSA pumping is not likely to reduce the likelihood of survival and recovery of TBS in the wild. TBS does not have critical habitat.

7. Incidental Take Statement

Section 9 of the ESA, and Federal regulation pursuant to section 4(d) of the ESA as amended, prohibit the take of endangered and threatened species, respectively, without special exemption. Take is defined as to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, collect, or to attempt to engage in any such conduct. Harm is further defined by the Service to include significant habitat modification or degradation that results in death or injury to listed species by significantly impairing essential behavior patterns, including breeding, feeding, or sheltering. Harass is defined by the Service as intentional or negligent act or omission which creates the likelihood of injury to listed species by annoying it to such an extent as to significantly disrupt normal behavior patterns which include, but are not limited to, breeding, feeding, and sheltering. Incidental take is defined as take that is incidental to, and not the purpose of, the carrying out of an otherwise lawful activity. Under the terms of sections 7(b)(4) and 7(o)(2) of the ESA, taking that is incidental to and not intended as part of the agency action is not considered to be prohibited taking under the Act provided that such taking is in compliance with an Incidental Take Statement.

The measures described below as reasonable and prudent measures and terms and conditions in this biological opinion are non-discretionary and must be undertaken by JBSA so that they become binding conditions of any condition of any grant or permit issued to JBSA, as appropriate, in order for the exemption in section 7(o)(2) to apply JBSA. JBSA-Fort Sam Houston, JBSA-Lackland, and JBSA-Randolph have a continuing duty to regulate the activity covered by this incidental take statement. If JBSA (1) fail to assume, implement, or adhere to the terms and conditions of the incidental take statement, and/or (2) fail to retain oversight to ensure compliance with these terms and conditions, the protective coverage of section 7(o)(2) may lapse. In order to monitor the impact of incidental take, JBSA must report the progress of the action and its impacts on the species to the Service as specified in the incidental take statement. [50 Code of Federal Regulations (CFR) §402.14(i)(3)].

Sections 7(b)(4) and 7(o)(2) of the ESA generally do not apply to the incidental take of listed plant species. However, protection of listed plants is provided to the extent that ESA prohibits the removal, reduction to, and possession of federally listed endangered plants or the malicious damage of such plants on areas under Federal jurisdiction, or the destruction of endangered plants on non-Federal areas in violation of State law or regulation or in the course of any violation of a State criminal trespass law.

Amount or extent of take anticipated

The Service expects that JBSA’s Edwards Aquifer groundwater withdrawals will incidentally take individuals of Peck’s cave amphipods, Comal Springs dryopid beetles, Comal Springs riffle beetles, San Marcos gambusia, fountain darters, and San Marcos salamanders. The Service is providing JBSA with an incidental take statement for: (1) Peck’s cave amphipod, (2) Comal

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Springs dryopid beetle, (3) Comal Springs riffle beetle, (4) San Marcos gambusia, (5) fountain darter, and (6) San Marcos salamander. We do not anticipate incidental take of Texas blind salamander.

This biological opinion does not authorize any form of take that is not incidental to the withdrawal of Edwards Aquifer groundwater by the JBSA, in the authorized water withdrawal amounts specified and in conjunction with other take minimizing measures described in this biological opinion. The reasonable and prudent measures and the terms and conditions from previous biological opinions are superseded by this biological opinion.

The Service does not anticipate the proposed action will incidentally take any Texas blind salamanders. Regarding other species in this consultation, Table 5 provides a summary of the amount of take anticipated by the proposed project.

Effect of Take

In the accompanying biological opinion, the Service determined that this level of anticipated take is not likely to result in jeopardy to the Peck’s cave amphipod, Comal Springs dryopid beetle, Comal Springs riffle beetle, San Marcos gambusia, fountain darter, San Marcos salamander, or Texas blind salamander species, or result in the destruction or adverse modification of critical habitat.

7.a. Reasonable and Prudent Measures

The Service believes that the reasonable and prudent measures presented below are necessary and appropriate to minimize the incidental taking authorized by this biological opinion.

1. The JBSA shall, to the maximum practicable extent, avoid and minimize adverse effects to the Peck’s cave amphipod, Comal Springs dryopid beetle, Comal Springs riffle beetle, fountain darter, San Marcos salamander, and Texas blind salamander.

2. JBSA shall continue to reduce its dependence on Edwards Aquifer groundwater within the time frame covered by this consultation (August 2013 to March 31, 2028) by implementing water conservation measures and using other alternative water sources to reduce Edwards Aquifer groundwater withdrawals.

3. JBSA shall actively engage in public outreach to reduce the effects of on and off-base activities in the San Antonio area and actively promote public information and education on water use, quantity, quality, and conservation efforts on and off-base. JBSA shall include in its annual report its outreach efforts and any progress made to conserve the Edwards Aquifer.

4. The JBSA shall report annually to the U.S. Fish and Wildlife Service, Austin Ecological Services Field Office, on its progress implementing this biological opinion.

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7.b. Terms and Conditions

In order to be exempt from the prohibitions of section 9 of the Act, JBSA must comply with the following terms and conditions, which implement the reasonable and prudent measures described above and outline required reporting/monitoring requirements. These terms are non discretionary.

1. JBSA shall implement all of the conservation measures described in Section 2 of this biological opinion including curtailing groundwater withdrawal according to its critical period management plan.

2. Monitor JBSA pumping and include in the annual report to the Service. Report shall provide: (a) daily withdrawals by water well (in either gallons per day or cubic feet per day) and (b) daily critical period designation.

3. Design and implement a voluntary program or partner with EAA, SAWS, and/or other organizations to educate and assist employees in achieving water conservation on base and off base at personal residences. Such program activities could include education and outreach on water conservation practices such as retrofitting with low flow toilets and shower heads or using xeriscaping as an alternative to water intensive landscaping practices.

4. The JBSA shall submit annual reports informing the Service of its progress implementing the Reasonable and Prudent Measures and Terms and Conditions set forth in this biological opinion. The report shall include a description of the activities have been implemented in the prior calendar year, an evaluation of the effectiveness of those activities, and notify the Service of any discretionary conservation recommendations which have been implemented. The reports shall include total daily, monthly, and annual (based on calendar year) groundwater withdrawal in kilogallons (kgal) for each JBSA well drawing from the Edwards Aquifer. Annual reports shall be sent to the U.S. Fish and Wildlife Service, 10711 Burnet Rd., Suite 200, Austin, TX 78758 and due June 1st of each year (for the previous calendar year) covered by this biological opinion.

The Service believes that no more than the numbers of individuals of each species shown in Table 5 will be incidentally taken as a result of the proposed action. The reasonable and prudent measures, with their implementing terms and conditions, are designed to minimize the impact of incidental take that might otherwise result from the proposed action. If, during the course of the action, this level of incidental take is exceeded, such incidental take represents new information requiring reinitiation of consultation and review of reasonable and prudent measures provided. The JBSA must immediately provide an explanation of the causes of taking and review with the Service the need for possible modification of the reasonable and prudent measures.

8. Conference Opinion on Proposed Revisions to Designated Critical Habitat

On July 17, 2007, the Center for Biological Diversity, Citizens Alliance for Smart Expansion, and Aquifer Guardians in Urban Areas provided the Service with a 60-day notice of intent to sue

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on the final critical habitat rules for a number of species, including Peck’s cave amphipod. On January 14, 2009, the plaintiffs filed suit in U.S. District Court for the Western District of Texas on issues related to sections 3(5)(A) and 4(b)(2) of the Act. On December 18, 2009, the parties filed a settlement agreement in which the Service agreed to submit to the Federal Register: (1) a revised proposed rule for designation of critical habitat for these species on or before October 17, 2012 and (2) a final rule for critical habitat on or before October 13, 2013. A proposed rule was published in the Federal Register in accordance with the settlement agreement, and public review and comment have been solicited (77 FR 64272).

The final rule will not be published during the required timeframe for this formal consultation; therefore, we are including an analysis of effects of the action on the proposed critical habitat for each of these three species in this conference opinion.

Differences between current designated and proposed critical habitat for CSI

The PCEs from the proposed revision of Critical Habitat for the Comal Springs dryopid beetle, Comal Springs riffle beetle, and Peck’s cave amphipod are similar to but slightly modified from the current PCEs. The proposed PCEs have been consolidated from five (originally) to three.

(1) Springs, associated streams, and underground spaces immediately inside of or adjacent to springs, seeps, and upwellings that include: (a) High-quality water with no or minimal pollutant levels of soaps, detergents, heavy metals, pesticides, fertilizer nutrients, petroleum hydrocarbons, and semi- volatile compounds such as industrial cleaning agents; and (b) Hydrologic regimes similar to the historical pattern of the specific sites must be present, with continuous surface flow from the spring sites and in the subterranean aquifer. (2) Spring system water temperatures that range from 68 to 75°F (20 to 23.4°C). (3) Food supply that includes, but is not limited to, detritus (decomposed materials), leaf litter, living plant material, algae, fungi, bacteria, other microorganisms, and decaying roots.

The most significant change between the previously designated and proposed critical habitat is the addition of a subsurface area for the Peck’s cave amphipod and Comal Springs dryopid beetle. The additional subsurface critical habitat is to capture the nearby (within 110 m of springs) parts of the aquifer where Peck’s cave amphipods and Comal Springs dryopid beetles may travel (See Table 6). A minor change is the inclusion of Comal Spring run No. 4 in the proposed revised maps of surface critical habitat for all three Comal Springs invertebrates. The surface and subsurface areas provide suitable water quality, water flow, and detritus, in short their essential physical and biological needs.

As stated above, the main difference in the proposed revised critical habitat is the addition of a subsurface component for two of the Comal Springs invertebrates. The proposed action, JBSA pumping, is located in Bexar County. It is not expected to have a discernible effect on the subsurface critical habitat and associated PCEs proposed for Peck’s cave amphipod or Comal Springs dryopid beetle at Comal Springs, Hueco Springs, or Fern Bank Springs.

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Effects of the action on the proposed revision to designated critical habitat for Peck’s cave amphipod

The proposed revision to designated critical habitat for Peck’s cave amphipod includes both the surface and subsurface areas associated with Comal Springs and Hueco Springs in Comal County, Texas

The proposed revision to designated critical habitat for Peck’s cave amphipod is a 50-ft distance from the shoreline of both Comal Springs and Hueco Springs (including several satellite springs that are located between the main outlet of Hueco Springs and the Guadalupe River) to include amphipod food sources in the root-water interfaces around spring outlets.

The effect of the proposed action is not anticipated to affect the hydrologic regime, water quality, water temperature, or food supply within the proposed critical habitat units at Comal and Hueco springs because any reduction in flows will be too small (1 to 2 percent) to alter significantly alter habitat conditions. The JBSA withdrawal of groundwater is likely to have a similar effect on the PCEs of proposed critical habitat as it would on the currently designated critical habitat analyzed in our biological opinion for the proposed action.

Effects of the action on the proposed revision to designated critical habitat for the Comal Springs dryopid beetle

The proposed revision to designated critical habitat for the Comal Springs dryopid beetle includes both the surface and subsurface areas associated with Comal Springs and Fern Bank Springs in Comal and Hays counties, Texas. The proposed critical habitat includes the surface habitat 50-ft from spring outlets and the subsurface habitat 360-ft from the spring outlets.

The effect of the proposed action is not anticipated to discernibly affect any of the CSDB PCEs including the hydrologic regime, water quality, temperature and food supply within the proposed surface and subsurface units at Comal and Fern Bank springs.

This is based primarily on the minor effect on flow estimated to occur at Comal Springs from JBSA pumping in Bexar County. Similarly, no adverse effects on Fern Bank Springs are anticipated. The effects of the proposed action on the proposed critical habitat are similar to those described for designated critical habitat in this biological opinion.

Effects of the action on the proposed revision to designated critical habitat for the Comal Springs riffle beetle

The proposed CSRB critical habitat consists of surface habitat in Comal and San Marcos Springs similar to the original designation.

“For the Comal Springs riffle beetle, we only identified surface critical habitat because this species’ habitat is primarily restricted to surface water, which is located in two

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impounded spring systems in Comal and Hays Counties, Texas. In Comal County, this aquatic beetle is found in various spring outlets of Comal Springs that occur within Landa Lake over a linear distance of approximately 0.9 mi (1.4 km). The species has also been found in outlets of San Marcos Springs in the upstream portion of Spring Lake in Hays County. However, populations of Comal Springs riffle beetles may exist elsewhere in Spring Lake (excluding a slough portion that lacks spring outlets), but sampling for riffle beetles at spring outlets within the lake has only been done on a limited basis. Excluding the slough portion that lacks spring outlets, the approximate linear distance of Spring Lake at its greatest length is 0.2 mi (0.3 km). Critical habitat unit boundaries for surface area were delineated using the same criteria as described above for the Comal Springs dryopid beetle.”

JBSA pumping is not expected to affect water temperatures within the aquifer nor springflow temperatures at Comal or San Marcos springs. The effects of the action will not affect the ability of designated critical habitat units from continuing to provide this primary constituent element.

The effects of the action will not destroy or adversely modify the ability of the revised designated critical habitat of the CSRB from providing the identified primary constituent elements required for the conservation of the species.

Conference Opinion Conclusion on Proposed Critical Habitat Revisions

After reviewing the current status, the environmental baseline, the effects of the action and the cumulative effects, it is the Service’s Conference Opinion that the action, as proposed, is not likely to destroy or adversely modify proposed critical habitat for the Peck’s cave amphipod, Comal Springs dryopid beetle, and Comal Springs riffle beetle. The main difference between the designated and proposed critical habitat units is the addition of subsurface critical habitat near occupied springs in the proposed revisions. JBSA pumping is not expected to adversely affect the subsurface habitats in our proposed critical habitat revisions.

This concludes the conference for the JBSA withdrawal of the Edwards Aquifer groundwater. You may ask the Service to confirm the conference opinion as a biological opinion issued through formal consultation if the critical habitat is revised. The request must be in writing. If the Service reviews the proposed action and finds that there have been no significant changes in the action as planned or in the information used during the conference, the Service will confirm the conference opinion as the biological opinion on the action and no further section 7 consultation will be necessary.

After revision of designated critical habitat for the Comal Springs dryopid beetle, the Comal Springs riffle beetle, or the Peck’s cave amphipod and any subsequent adoption of this conference opinion, the JBSA shall request reinitiation of consultation if: (1) the amount or extent of incidental take is exceeded; (2) new information reveals effects of the agency action that may affect species or critical habitat in a manner or to an extent not considered in this conference opinion; (3) the agency action is subsequently modified in a manner that causes an effect to the species or critical habitat that was not considered in this conference opinion; or (4) a new species is listed or critical habitat designated that may be affected by the action.

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The incidental take statement provided in this conference opinion does not become effective until the proposed critical habitat is designated and the conference opinion is adopted as the biological opinion issued through formal consultation. At that time, the action will be reviewed to determine whether any designated critical habitat with be destroyed or adversely modified. Modifications of the opinion may be appropriate. No take of the habitat may occur between the designation of critical habitat and the adoption of the conference opinion through formal consultation, or the completion of a subsequent formal consultation.

9. Conservation Recommendations

Section 7(a)(1) of the Act directs Federal agencies to use their authorities to further the purposes of the Act by carrying out conservation programs for the benefit of endangered and threatened species. Conservation recommendations are discretionary agency activities to minimize or avoid adverse effects of a proposed action on listed species or critical habitat, to help implement recovery plans, or to develop information. The Service makes these conservation recommendations:

1. The Service believes that in the foreseeable future as water conservation measures are implemented, the risk to species survival can be reduced by implementing a drought management plan that further curtails groundwater withdrawal from the Edwards Aquifer. These measures may include such things as:

A. improving the condition of species and habitat in the wild so that they are in better condition going into the low flows and so that the relative portion of the population impacted will be less; an example of improving the condition of a species would be to reduce parasites and pathogens; an example of improving fountain darter habitat would be to increase the areal extent of (restore) native aquatic macrophytes in the Comal and upper San Marcos rivers.

B. answering information needs to better manage the aquifer for conservation of listed species, and;

2. Provide material support for ex situ refugia for covered species to maintain captive populations and enhance restoration opportunities.

3. Further reduce water dependency beyond the levels set in this biological opinion. (Task 2.31 of the 1996 Revised Recovery Plan for the San Marcos and Comal Springs and associated aquatic ecosystems.

4. Support improvements to the Edwards Aquifer hydrologic modeling, including modeling the Trinity Aquifer’s interaction with the Edwards Aquifer, and estimating Hueco Springs discharge.

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5. Assist with research on habitat and flow requirements ofthe listed species as needed.

6. Encourage partnerships among the JBSA and other Edwards Aquifer users, such as local, regional, state, and Federal agencies and other private or public entities for cooperative efforts to conserve the Edwards Aquifer waters in a way that provides for continuous spring flows needed by the endangered and threatened species.

In order for the Service to be kept informed of actions minimizing or avoiding adverse effects or benefitting listed species or their habitats, the Service requests notification of the implementation of any conservation recommendations.

10. Reinitiation Requii'ements

This concludes formal consultation on the ongoing and proposed actions by JBSA. As provided in 50 CFR 402.16, reinitiation of formal consultation is required where discretionary Federal agency involvement or control over the action has been retained (or is authorized by law) and if: (l) the amount or extent of incidental take is exceeded; (2) new information reveals effects of the agency action that may affect listed species or critical habitat in a mam1er or to an extent not considered in this biological opinion, (3) Department of Defense actions are subsequently modified in a manner that causes an effect to a listed species or critical habitat that was not considered in this biological opinion; or (4) a new species is listed or critical habitat designated that may be affected by this action. In instances where the amount or extent of incidental take is exceeded, any operations causing such take must cease pending reinitiation.

In future communications on JBSA's use of the Edwards Aquifer, please refer to consultation number 02ETAU00-20!3-F-0060. If we may be ofany assistance, please contact Tanya Sommer at (512) 490 0057 extension 222.

---~~n Zenenner Field Supervisor Biological Opinion for JBSA Edwards Aquifer Use Page 77

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Biological Opinion for JBSA Edwards Aquifer Use

Table 1. The proposed JBSA Edwards Aquifer water use for normal and critical period (drought) conditions (From JBSA 2012, BA Chapter 4, Table 4-4).

Bexar Index Well San Marcos Percent Comal Springs Monthly (J-17) Springs Reduction of Critical Springflow Maximum Trigger, Springflow JBSA Period Trigger Groundwater Water Level Trigger Edwards Stage in Cubic Feet Withdrawal, in Elevation in Cubic Feet Groundwater per Second * in acre-feet Feet, above per Second * Withdrawal msl *

Normal >660 >225 >96 0% 1,001.00

I <660 <225 <96 20% 800.80

II <650 <200 <80 30% 700.70

III <640 <150 N/A 35% 650.65

IV <630 <100 N/A 40% 600.60

<45 * V <625 N/A 44% 560.56 <40 †

* Based on a 10 day moving average of trigger (level for J-17, daily mean discharge for springs) † Based on a 3 day moving average of trigger (Comal Springs daily mean discharge)

Biological Opinion for JBSA Edwards Aquifer Use

Table 2. General Distribution of Endangered and Threatened Species Dependent on the Edwards Aquifer. P indicates presence. Aq indicates these species may also be found in nearby parts of the Edwards Aquifer including wells, wet caves, and springs. X indicates San Marcos gambusia is likely extinct throughout its historic range.

Comal Springs Fern Bank San Marcos Springs Upper San Marcos Species Comal River Hueco Springs and Landa Lake Springs and Spring Lake River

Texas wild‐rice P P

Comal Springs dryopid ◙ beetle P Aq P

Comal Springs riffle beetle P P

Peck’s cave amphipod BP Aq P

fountain darter P P P P

San Marcos gambusia X

San Marcos salamander P P

Texas blind salamander BP Aq

Biological Opinion for JBSA Edwards Aquifer Use

Table 3. Estimated Size of Populations of Comal Springs Invertebrates in Comal Springs System

COMAL COMAL PERCENT AREA M2 OF PECK'S CAVE SPRINGS SPRINGS COMAL COMAL OF ZONE SPRING AMPHIPOD DRYOPID RIFFLE PECK'S COMAL SPRINGS Area SPRINGS SPRINGS ZONE 2 WITH DOMINATED DENSITY BEETLE BEETLE CAVE ZONE M DRYOPID RIFFLE SPRING HABITAT IN INDIVIDUALS DENSITY DENSITY AMPHIPOD BEETLE BEETLE HABITAT ZONE PER M 2 INDIVIDUALS INDIVIDUALS PER M 2 PER M 2

SPRING RUN 1 A 1,310 100% 1,310 6.6 1.0 3.3 8,648 1,310 4,324 UPPER

SPRING RUN 1 B 590 10% 59 6.6 1.0 3.3 389 59 195 LOWER

SPRING RUN 2 C 101 100% 101 6.6 0.5 2.9 670 52 1,200 UPPER

SPRING RUN 2 D 408 5% 20 6.6 0.1 0.0 135 2 1 LOWER EMBAYMENT (Below E 2,934 1% 29 6.6 0.0 2.9 194 0 85 Confluence of SR 1 and SR 2)

F SPRING RUN 3 1,165 34% 397 6.6 0.1 3.7 2,620 36 1,473

WESTERN SHORELINE G 540 70% 378 6.6 0.5 2.9 2,495 193 1,077 (West of upper Pecan Island)

SPRING RUN 6 H 95 100% 95 6.6 0.5 2.9 627 48 271 (on Spring Island)

Biological Opinion for JBSA Edwards Aquifer Use

Table 3. Estimated Size of Populations of Comal Springs Invertebrates in Comal Springs System

NEAR SPRING ISLAND I 4,790 50% 2,395 6.6 0.5 2.9 15,807 1,221 6,826 (EXCLUDES SPRING RUN 6)

SPRING RUN 5 J (Nolte Village 49 100% 49 6.6 0.5 0.0 323 25 0 Apts)

SPRING RUN 4 K 540 50% 270 6.6 0.5 0.0 1,783 138 0 (Near NBU Yard)

COMAL SPRINGS Total (Surface) 12,523 40.8% 5,105 6.6 33,691 3,084 15,451 SYSTEM TOTAL (A - K)

Total for SR 1, SR 3,574 1,888 6.6 12,462 1,458 7,192 2 and SR 3

Biological Opinion for JBSA Edwards Aquifer Use

Table 4. Incidental Take Calculations for Comal Spring Invertebrates, Fountain Darter, and San Marcos Salamander

Incidental Take Attributed to 1.2 Percent of Estimated Incidental Take One Low Flow Event 1.2 Percent of Incidental Incidental Take Incidental Take Population Size in Attributed to Not part of Drought of Record Take Attributed to One Estimated Attributed to Determination Species Comal Spring Drought of Record (Non-DOR)) in Comal Spring Runs Low Flow Event Non- Population Size Drought of Record for JBSA Edwards Runs Event Lasting 7 No. 1, 2 & 3 DOR in Comal Spring Event Lasting 7 Use No. 1, 2 & 3 Years (Decrease Estimated as ½ of Local Runs No. 1, 2 & 3 Years Surface Population)

Peck's cave amphipod 33,691 12,462 17,360 208 6,231 75 283 Comal, surface

Comal Springs dryopid beetle 3,084 1,458 1,471 18 729 9 26 Comal, surface

Comal Springs riffle beetle 15,451 7,192 10,739 129 3,596 43 172 Comal, surface

Incidental Take Attributed to 1.2 Percent of 1.2 Percent of Incidental Estimated Incidental Take One Low Flow Event Incidental Take Take Attributed Incidental Take Population Size in Attributed to Non-Drought of Record Estimated Attributed to to One Low Flow (Non- Determination Species Comal Spring Drought of Record (Non-DOR) For Entire River System Population Size Drought of Record DOR) Event for JBSA Edwards Runs Event Lasting 7 Comal System < 100 CFS Event Lasting 7 for Entire Spring Use No. 1, 2 & 3 Years San Marcos System < 85 CFS Years System Decrease Estimated at ¼ of Population

Fountain darter Comal Spring System 774,000 462 735,000 8,820 193,500 2,322 11,142 Spring Runs, Landa Lake & River Channels

Fountain darter San Marcos Spring System 894,000 n a 450,000 5,400 223,500 2,682 8,082 Spring Lake and San Marcos River downstream to Blanco R.

San Marcos salamander Spring Lake and 365,750 n a 233,361 2,800 91,438 1,097 3,898 Nearby Areas Downstream

Biological Opinion for JBSA Edwards Aquifer Use

Table 5. Incidental Take Summary for Selected Species

Table 5. Incidental Take Summary for Comal Spring Invertebrates, Fountain Darter, and San Marcos Salamander

Incidental Take Determination Species for JBSA Edwards Aquifer Use

Peck's cave amphipod 283 Comal, surface

Comal Springs dryopid beetle 26 Comal, surface

Comal Springs riffle beetle 172 Comal, surface

Fountain Darters 19,224 Comal and San Marcos Spring Systems

San Marcos salamander Spring Lake and 3,898 Nearby Areas Downstream

Biological Opinion for JBSA Edwards Aquifer Use

Table 6. A Comparison 2007 2012 of Original Designated Original CH Proposed 2012 Proposed and Proposed Revised Unit (Surface Revised CH Revised CH Critical Habitat (CH) for Only) Surface Subsurface (acres) the Comal Springs (acres) (acres) Invertebrates

Peck's Cave Comal 38.1 37.9 124.3 Amphipod

Peck's Cave Hueco 0.4 0.4 13.5 Amphipod

PCA total 38.5 38.4 137.8

Comal Springs Comal 38.1 37.9 124.3 Dryopid Beetle Comal Springs Fern Bank 1.4 1.4 15.0 Dryopid Beetle CSDB 39.5 39.4 139.3 total Comal Springs Riffle Comal 19.8 37.9 n a Beetle

Comal Springs Riffle San Marcos 10.5 16.2 n a Beetle CSRB 30.3 54.1 n a total

Biological Opinion for JBSA Edwards Aquifer Use

Figure 1. Action area for JBSA and Edwards Aquifer withdrawals.

Figure 1. Action Area Joint Base San Antonio Southern Edwards Aquifer Bexar, Comal, and Hays Co., TX and Springs Supporting Endangered Species

Edwards Aquifer - EAA .. Artesian Zone Contributing Zone

Recharge Zone .. Transition in Recharge Zone D Joint_Base_San_Antonio

D ACTION_AREA

~ M il es 0 3 6 12 18 24

Biological Opinion for JBSA Edwards Aquifer Use

Figure 2. Comal Springs and Landa Lake Showing Spring Habitats Supporting Comal Springs Invertebrates (CSI)

Figure 2.

Peck's Cave Amphipod Comal Springs Dryopid Beetle Comal Springs Riffle Beetle Habitat Patches N CSI Habitat Name - A· Spring Run 1 (Upper) - B· Spring Run 1 (lower) - C ·Spring Run 2 (Upper) j - D ·Spring Run 2 (lower) - E- Embayment - F· Spring Run 3 - G- Western Shoreline - H • Spring Run 6 (On Spring Island) I - Spring Island (Nearby)

0 200 400 800 Feet

0 80 160 320 Meters

Biological Opinion for JBSA Edwards Aquifer Use

Figure 3. Comal Springs as mapped in April, 2012 by Chad Norris (TPWD) and others (Norris 2013).

Comal Springs (Provisional) tv Actual and Potential Habitat for Peck's Cave Amphipod Comal Springs Dryopid Beetle Comal Springs Riffle Beetle Habitat Patches (Lettered) I • ComaI Springs (provisional) TPW CN

CO MAL SPRING RUN 2

o 200 400 800 Feet

0 80 160

Biological Opinion for JBSA Edwards Aquifer Use

CCHMI SpringRow COINI Sprtngnow Date PNMI PhaMI Corr al S~rin~sMod~ u~Ph se l 350 (cf•l (C-fs) -f-- n Aug-1183 78 88 s :::~:: ~ -I .. -t--.-t---+ --1-' sl Joo,u~~~-~··,~·--~·oo~~~ ~ ~t~-1--r-t-t-~J

f 2~~+-+-1-~-~ hH~hr+-'+-+-~~~~~

t 200 t-.-l---t---t--t----t-1~ - - ltt- ll~ft l ] J..!_ __ 1l 1~

400

1- I If " I

Figure 4. Simulated Comal Springs Discharge (Monthly Mean) with Historic Recharge Sequence and EARIP HCP Aquifer Phase I (2013 -2021)(Current) Management and Phase II (2021 – 2028)(Future) Management.