fish wll.dlife service united states department ofthe interior · fish & wll.dlife . service ....

u.s. FISH & Wll.DLIFE

SERVICE

United States Department of the 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. Pecks cave amphipod ...................................................................................................................................... 15







c. Comal Springs dryopid beetle .......................................................................................................................... 20







d. Comal Springs riffle beetle .............................................................................................................................. 25







e. San Marcos gambusia ....................................................................................................................................... 29







f. fountain darter .............................................................................................................................................. 34







g. San Marcos salamander ................................................................................................................................... 40







h. Texas blind salamander.................................................................................................................................... 44







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. Pecks cave amphipod ...................................................................................................................... 53

Effects of action on the Pecks cave amphipod ....................................................................53


iii. Comal Springs dryopid beetle ......................................................................................................... 56

Effects of action on the Comal Springs dryopid beetle ........................................................56


iv. Comal Springs riffle beetle ............................................................................................................. 58

Effects of action on the Comal Springs riffle beetle .............................................................58


v. San Marcos gambusia ....................................................................................................................... 60

Effects of action on the San Marcos gambusia .....................................................................60


vi. Fountain darter ................................................................................................................................ 61

Effects of action on the fountain darter ................................................................................61


vii. San Marcos salamander ................................................................................................................. 63

Effects of action on San Marcos salamander ........................................................................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 Pecks 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 Pecks 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 JBSAs 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


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 20082012 was 92,784.

The 20082012 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, JBSAs 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.


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 JBSAs 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 JBSAs 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


(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


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 zones 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 Pecks 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.


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 (Pecks 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 71F (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


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 71F (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).


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 JBSAs proportion of overall Edwards Aquifer pumping.

The Service supports the principles guiding the Department of Defenses Legacy program: stewardship, leadership, and partnership. JBSA has already shown its stewardship in water conservation. Consistent with the Acts section 7(a)(1)(A) directive to use their authorities by carrying out programs for the conservation of threatened and endangered species, we encourage


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, Pecks 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


Doyle 2004). Water from the Edwards Aquifer contains relatively high levels of dissolved carbon dioxide due to the calcium carbonate makeup of the regions 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 waters 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


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 Rivers 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 plants 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 waters 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


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), Becketts 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.


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.


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 Areas 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.


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 0.9F 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 4F. Vaughan (1986) reported a constant springflow temperature of 70.7F, with temperature ranges of 68.7F in February to 77.9F 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. Pecks cave amphipod

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


Pecks cave amphipod is a subterranean-adapted aquatic crustacean first collected in 1964 at


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. Pecks cave amphipod was listed as endangered on December 18, 1997 (62 FR 66295).

Some evidence suggests Pecks 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.

Pecks 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 Pecks 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 Pecks 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.


Pecks 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.


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

The Pecks cave amphipods specialized subterranean and aquatic adaptations indicate that the species evolved in subterranean areas within the aquifer. However, the vast majority of the Pecks 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 Pecks cave amphipods and other Comal Springs invertebrates. Table 3 provides the size of these areas, the estimated density of Pecks 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 Pecks cave amphipod was collected at Hueco Springs was August 16, 2003. The Pecks 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 Pecks cave amphipod, and that this decline is due primarily to human activities including withdrawal of water from the Edwards Aquifer (62 FR 66295).

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 are considered threats to water quality. 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.

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 Pecks cave amphipods will be reduced and areas associated with higher elevation springs that are currently suitable will be dewatered and become unsuitable.


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 Pecks cave amphipod populations in that period.

Survival Needs and Recovery Criteria

The chief survival need identified in the Pecks cave amphipod listing rule is conservation of suitable habitat to sustain populations of the species. The conservation of Pecks cave amphipod habitat includes maintenance of water quality and continuous natural springflow. No Recovery Plan has been finalized for the Pecks 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

Pecks 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 Pecks cave amphipods has been authorized under these consultations. None of these consultations resulted in a determination that the considered actions would jeopardize the Pecks cave amphipod or result in destruction or adverse modification of designated critical habitat.

On January 8, 2010, the Texas Parks and Wildlife Commission placed Pecks 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 Pecks cave amphipod or its habitat.

Critical Habitat

Critical habitat for Pecks 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.


Designated critical habitat for the Pecks 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 lakes 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 Pecks 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 Pecks 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 75F (20 to 24C); 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 74.1F), and food supplies described in the critical habitat designation are present.


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.


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 Stanfords 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.


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.


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) (BIOWEST 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 beetles 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,

fish wll.dlife service united states department ofthe interior · fish & wll.dlife . service ....

Documents