# Aransas Project v. Shaw

> District Court, S.D. Texas · March 11, 2013 · 930 F. Supp. 2d 716

URL: https://www.frixlaw.com/law-library/cases/8706784

## Case

- **Full name:** The ARANSAS PROJECT v. Bryan SHAW
- **Court:** District Court, S.D. Texas
- **Decided:** March 11, 2013
- **Citations:** 930 F. Supp. 2d 716; 43 Envtl. L. Rep. (Envtl. Law Inst.) 20053; 2013 U.S. Dist. LEXIS 33258; 2013 WL 943780
- **Precedential status:** Published
- **Opinion:** Opinion of the court by Jack
- **Judges:** Jack
- **Cited by:** 3 later opinions in the Frix Law Library

## Citator (automated)

- No negative treatment found by the automated citator. That is not the same as a confirmation that the case is good law; read the citing cases.
- Full citator and citing cases: https://www.frixlaw.com/law-library/cases/8706784

## How later opinions describe it (automated extraction)

- stating that ordinary requirements of proximate causation apply

## Opinion text

MEMORANDUM OPINION AND VERDICT OF THE COURT
JANIS GRAHAM JACK, Senior District Judge.
This case was tried to the Court over an eight-day period on December 5, 6, 7, 8, 9, 13, 14, and 15, 2011. 1 As required by Rule 52(a) of the Federal Rules of Civil Procedure, the Court makes the following findings of fact and conclusions of law thereon. 2
Table of Contents
I. INTRODUCTION.......................................................722
II. STATUTORY FRAMEWORK.............................................726
A. The Endangered Species Act..........................................726
1. ESA § 9 prohibits “takes” of endangered species.....................726
2. ESA § 10 addresses incidental takes................................727
III. FINDINGS ON STANDING AND JURISDICTION.........................727
A. Standing............................................................727
1. Injury in fact....................................................728
2. Redressability ...................................................729
3. Causation.......................................................730
B. Burford abstention...................................................731
1. Senate Bill 3.....................................................733
2. Texas surface waters..............................................737
IV. FINDINGS ON CAUSATION.............................................744
A. Court’s findings as to witness expertise and credibility....................744
B. TCEQ’s water diversions reduce freshwater inflows to the Refuge..........745
1. Trungale established permitted water diversions lower inflows to
Refuge........................................................745
2. Trungale’s findings anticipated.....................................747
3. Dr. Ward’s modeling not reliable...................................748
4. Dr. Montagna’s observations and studies confirmed Trungale’s
modeling......................................................749
5. Dr. Davis’ modeling...............................................751
C. Higher salinities adversely affect blue crabs and wolfberries...............752
1. Dr. Montagna on salinity preferences of blue crabs ...................752
2. Dr. Miller’s blue crab data.........................................753
3. Wolfberry production.............................................754
4. Observations and measurements concerning blue crab abundance and wolfberry availability in 2008-2009 ............................ 754
D. Statistical modeling confirms higher salinities are associated with
higher crane mortality on the Refuge.................................754
E. At least 23 Whooping Cranes died on the Refuge in 2008/2009 .............756
1. Counting cranes is rooted in crane behavior..........................757
*722 2. Tom Stehn determined peak population numbers for the USFWS.....758
3. Crane mortality counts............................................760
4. Defendants’and intervenors’objections to mortality counts............762
F. Food stress caused the death of at least 23 cranes........................764
1. Necropsy findings................................................764
2. Opinions of the crane experts......................................764
3. Defendants and intervenors failed attempt to disprove food stress was cause of cranes’ death.......................................766
(a) Dr. Stroud...................................................766
(b) Dr. Slack....................................................767
(c) Dr. Porter...................................................768
G. Motion to reopen and the Abundance Survey............................769
1. Population versus mortality........................................769
2. Information in Abundance Survey conflicts with trial evidence..........770
(a) Territoriality.................................................770
(b) Peak Abundance..............................................771
(c) The Abundance Survey is preliminary...........................772
(d) No underlying data ...........................................773
(e) Error rate of the Abundance Survey is unacceptable...............774
IV. INJUNCTIVE AND OTHER RELIEF ....................................775
A. The ESA allows for injunctive relief, and provides for a relaxed standard in granting it..............................................775
B. An ITP is an appropriate remedy in this case............................776
1. Dr. Sunding’s economic analysis....................................779
IV. COURT’S ADDITIONAL FINDINGS OF PACT............................780
V. COURT’S CONCLUSIONS OF LAW......................................782
VI. DECLARATORY RELIEF, ITP, AND HCP ORDERED.....................788
COURT’S EXHIBIT 1: MAP OF AWB CRANES’ HABITAT........................790
I. INTRODUCTION.
In the annals of conservation, the return of the Whooping Crane from the brink of extinction is one of the most fabled stories. In the 1940’s, less than fifteen of these remarkable birds — the tallest in North America and the rarest species of crane in the world — remained. With the creation of wildlife refuges and other conservation efforts, the population of the birds has slowly risen to, including both those in captivity and those not in captivity, to around 500 birds. At issue here is the threat of extinction to the non-captivity population of around 300. However, the “whoopers” are still at risk, as development and environmental issues continue to threaten their habitat.
This case concerns the world’s only self-sustaining, wild Whooping Crane population, known as the “AWB” flock, 3 and its winter home in South Texas at the Aransas National Wildlife Refuge (the “Refuge”), and surrounding estuarine areas that comprise the AWB cranes’ critical winter habitat. 4 The AWB cranes normal *723 ly begin to arrive at their winter habitat in late October, and depart in early April of the following year.
The Aransas Refuge is located midway along the Texas Gulf coast, about 140 miles south of Houston and 50 miles north of Corpus Christi. 5 The cranes’ wintering grounds are comprised of approximately 9,000 hectares of salt flats on the Refuge itself and also on adjacent islands, including the Blackjack Peninsula, San Jose Island, and Matagorda Island. 6 The area is bordered on the east by the Gulf of Mexico, receiving daily impulses of salt water with the changing of the tides.
The Refuge receives freshwater inflows from primarily two river sources, the San Antonio and the Guadalupe, each located to the north and slightly west of the area. 7 The San Antonio river flows into the Guadalupe river system, and the Guadalupe river flows directly into the Refuge, emptying into the San Antonio bay. The area where the freshwater enters the Refuge is referred to correctly as the “Guadalupe estuary,” but it is known also as the “San Antonio bay.” 8 The San Antonio and the Guadalupe river systems emerge from underground springs near San Antonio and run 250 miles southeast where they join together just before entering the San Antonio bay and flow into the AWB flock’s winter habitat, that extends slightly north of the Refuge. 9 These freshwater inflows come from a combination of spring flows and rainfall. Id.
Whooping Cranes face extinction. Indeed today, it is estimated that only 500 Whooping Cranes exist worldwide. In 1967, the United States listed the Whooping Crane as threatened with extinction, 32 Fed.Reg. 4001 (Mar. 11, 1967), and in 1970, they were listed as endangered, 35 Fed. Reg. 16047 (Oct. 13, 1970). In 1973, both of these classifications were “grandfathered” into the Endangered Species Act. 16 U.S.C. § 1531 et seq., 87 Stat. 884 .
Beginning in 1950, the United States Fish & Wildlife Service (USFWS) employed aerial surveys to provide an annual census of how many AWB cranes arrived at the Refuge in the fall, and how many departed in the spring. Mr. Tom Stehn, a USFWS biologist, worked at the Refuge for over 29 years, and personally developed and implemented a method to count the individual birds of the AWB flock utilizing the cranes’ well-documented behaviors of site fidelity, site tenacity, and crane *724 territoriality. 10 Because specific birds returned to their specific locations, Mr. Stehn was able to map their territories and to confirm their presence or absence with weekly aerial surveys. 11 Based on his intimate knowledge of the AWB crane and his mapping of their territories, Mr. Stehn concluded that, at the start of the 2008 winter season, the AWB flock had grown to its peak number of 270 birds, plus or minus 2 to 3 percent.
During the 2008-2009 winter, there was a severe drought. As the winter progressed, the AWB cranes began to demonstrate unusual behavior. For example, parents would deny their juveniles food, and the birds began venturing out of their specific territories in search of food and fresh water. When the cranes first arrive at the Refuge, it is normal for the parents to feed the juvenile. The juveniles’ beaks are soft and tender, and it is necessary for the parent to break the shell and feed the crab to the begging juvenile. As the winter progresses, the parent pulls the crab from the water, kills it, and leaves it for the juvenile. During the 2008-2009 winter, Dr. Chavez-Ramirez observed a parent aggressively pushing his juvenile away from a crab that had been caught. He had never seen a parent deny food to a begging juvenile. Such behavior indicates that the parent was under food stress. The birds’ behavior was so alarming that Mr. Stehn contacted Dr. Chavez-Ramirez, a biologist with two decades of field research on the AWB cranes and a member of the International Whooping Crane Recovery Team, and asked him to visit the Refuge and observe the cranes. Dr. Chavez-Ramirez was equally troubled and concerned with his observations of the cranes’ behavior. Both he and Mr. Stehn observed that the lack of freshwater inflows had increased salinities across the Refuge. These hyper-saline conditions, verified by field measurements, led to a decrease in blue crabs and wolfberries, the staple diet of the AWB flock. This food shortage led to bird emaciation, stress behavior, and an over-all decline in bird health. That is, without proper freshwater inflows, the AWB’s critical habitat had been thrown out of balance, with ramifications up and down the food chain. That winter, at least 23 AWB cranes, or 8.5% of the AWB flock, died at the Refuge. Another 34 birds that left Texas in spring, failed to return in fall.
After news of the high crane mortality in the 2008-2009 winter became known, certain environmentalists, local coastal business owners, bird enthusiasts, and others formed “The Aransas Project,” (“TAP”), a Texas nonprofit corporation. The TAP members have a direct interest in the AWB Whooping Cranes and the ecological health of the San Antonio, Car *725 los, Mesquite, and Aransas bays that connect to the Refuge.
The State of Texas owns its surface water, and this includes the water in the Guadalupe and the San Antonio River systems. Under Texas law, freshwater capture and use is regulated by the Texas Commission on Environmental Quality (TCEQ), a State agency. Through its permit process and regulatory powers, the TCEQ can affect the availability of freshwater to users along the river system.
Prior to filing this lawsuit, TAP petitioned the TCEQ for a water permit to require a certain amount of freshwater to remain instream in the Guadalupe and San Antonio river systems to ensure that sufficient amounts of freshwater reached the Refuge and surrounding areas adjacent to the San Antonio bay that comprise the critical habitat of the AWB cranes. TAP’s permit request was denied, and on December 7, 2009, TAP gave notice of its intent to sue.
On March 10, 2010, TAP filed this lawsuit alleging that the TCEQ defendants had violated Section 9 of the Endangered Species Act (ESA), 16 U.S.C. § 1531 et seq., by failing to properly manage freshwater inflows into the San Antonio and Guadalupe bays during the 2008-2009 winter, causing an unlawful “take” of AWB cranes. (D.E. 1). TAP maintains that the TCEQ defendants’ water management practices during 2008-2009, combined with the severe drought, drastically modified the AWB cranes’ critical habitat making it hyper-saline. In turn, the hyper-saline conditions caused a reduction in the availability of wolfberries and blue crabs, the cranes’ primary food resources, as well as in fresh drinking water. The lack of food and freshwater caused the cranes to become emaciated and to engage in stress behavior. Emaciation led to increased illness and disease susceptibility, and the cranes’ unusual stress behaviors, including leaving the safety of their site territories, contributed to increased predation. In total, the adverse modification of the cranes’ critical habitat effectively caused the death of at least 23 Whooping Cranes that winter season, constituting a “take” under the ESA.
TAP named as defendants TCEQ officials Bryan Shaw, Buddy Garcia, Carlos Rubinstein, and Mark Vickery, and also, the South Texas Watermaster, A1 Segovia. 12 The Guadalupe-Bianco River Authority (GBRA) was granted leave to intervene. (D.E. 31, 35). Numerous other parties sought leave to intervene: Union Carbide Corporation (D.E. 45); Texas Farm Bureau (D.E. 51); Texas Chemical Council (D.E. 53); San Antonio Water System (D.E. 59); San Antonio City Public Service (D.E. 70); and the San Antonio River Authority (SARA) (D.E. 110). The Court granted Texas Chemical Council’s motion to intervene, but denied the others. 13 (D.E. 86, 112). On appeal, the Fifth Circuit allowed the intervention of the SARA, but affirmed the denial of intervention of the other parties. (D.E. 182, 183).
*726 Through this lawsuit, TAP is requesting declaratory and injunctive relief to ensure that the AWB flock has sufficient water resources to prevent future “takings.” (D.E. 1 at 32-33).
II. STATUTORY FRAMEWORK.
A. The Endangered Species Act.
Enacted in 1973, the Endangered Species Act (“ESA”) is an attempt to prevent the further elimination of animal species in the United States and to help those animal populations to increase. See 16 U.S.C. § 1531 et seq. The ESA’s stated purposes are “to provide a means whereby the ecosystems upon which endangered species and threatened species depend may be conserved ... [and] to provide a program for the conservation of such endangered species and threatened species.” 16 U.S.C. § 1531 (b). The plain intent of Congress in enacting this statute was “to halt and reverse the trend towards species extinction, whatever the cost.” Tennessee Valley Authority v. Hill, 437 U.S. 153, 184 , 98 S.Ct. 2279 , 57 L.Ed.2d 117 (1978).
1. ESA § 9 prohibits “takes” of endangered species.
Under the ESA, the Secretary of the Interior (“Secretary”) is required to promulgate regulations listing those species of animals that are “threatened” or “endangered” under specified criteria, and to designate their “critical habitat.” 16 U.S.C. § 1533 . Section 9 of the ESA prohibits “takes” of all listed endangered species. 16 U.S.C. § 1531 (a)(4)(B); 50 C.F.R. § 17.31 ; 55 Fed.Reg. 26114 (June 26, 1990). 14 The term “take” is defined as actions that “harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect,” a protected species. 16 U.S.C. § 1532 (19). The term “harm” includes “significant habitat modification or degradation where it actually kills or injures wildlife by significantly impairing essential behavioral patterns, including breeding, feeding or sheltering.” 50 C.F.R. § 17.3 ; Babbitt v. Sweet Home Chapter of Communities for a Great Oregon, 515 U.S. 687 , 115 S.Ct. 2407 , 132 L.Ed.2d 597 (1995). The term “harass” means “an intentional or negligent act or omission which creates the likelihood of injury to wildlife by annoying it to such an extent as to significantly disrupt normal behavioral patterns which include, but are not limited to, breeding, feeding, or sheltering.” 50 C.F.R. § 17.3 . Congress intended to define “take” in the “broadest possible manner to include every conceivable way” in which any person could harm or kill wildlife. S.Rep. No. 307, 93rd Cong., 1st Sess. 1, reprinted in 1973 U.S.Code Cong. & Admin. News 2989, 2995. In this case, the crux of TAP’s argument is that the TCEQ’s actions and inactions in managing water diversions along the San Antonio and Guadalupe River systems caused “harm” to the endangered Whooping Cranes, by actually injuring and killing 23 birds. 50 C.F.R. § 17.3 (the “harm” regulation).
The ESA’s prohibition against “takes” governs both the actions, and failure to act, by all “persons,” including any “officer, employee, agent, department, or instrumentality of ... any State.” 16 U.S.C. § 1532 (13). The ESA prohibitions apply to actions by state agencies where their regulatory programs approve actions by third parties that contribute to causing the take. E.g., Animal Welfare Inst. v. Martin, 623 F.3d 19 (1st Cir.2010) (citizens could challenge Maine’s authorization of foothold traps that harmed lynx); Strahan *727 v. Coxe, 127 F.3d 155 (1st Cir.1997) (challenging Massachusetts’ licensing of gill-net and lobster pot fishing as harming northern Right Whale); Loggerhead Turtle v. County Council of Volusia County, 148 F.3d 1231 (11th Cir.1998) (ESA applies to citizen’s challenge of county’s refusal to ban beach driving during sea turtle nesting season); and Defenders of Wildlife v. EPA, 882 F.2d 1294 (8th Cir.1989) (challenging EPA and Secretary of Interior’s permitting of strychnine pesticides and rodenticides).
Section 9 prohibits indirect as well as deliberate “takes” of endangered species. Babbitt, 515 U.S. at 700 , 115 S.Ct. 2407 ; Strahan, 127 F.3d at 163 . Ordinary requirements of proximate causation apply. Babbitt, 515 U.S. at 700, n. 13 , 115 S.Ct. 2407 (O’Connor, J., conc.); see also Loggerhead Turtle, 148 F.3d at 1251 n. 23 (“proximate cause is not the same thing as a sole cause,” citing Cox v. Administrator United States Steel & Carnegie, 17 F.3d 1386, 1399 (11th Cir.1994)). In fact, this Court has previously recognized in this case that proximate cause exists where a defendant government agency authorized the activity that caused the take. (See D.E. 270, 835 F.Supp.2d at 263-64).
2. ESA § 10 addresses incidental takes.
Following the ESA’s enactment, it became apparent that certain activities might result in an unintended take of an endangered species. For example, clearing certain acreage for development might destroy the habitat of a protected species of bird. Thus in 1982, Congress amended the ESA to authorize the issuance of permits allowing the take of a protected species if the take is incidental to otherwise lawful private actions. 16 U.S.C. § 1539 (a). Section 10 of the ESA provides, “The secretary may permit, under such terms and conditions as he shall prescribe,” any incidental taking otherwise prohibited by Section 9 that will not “appreciably reduce” 'the likelihood that the species will survive and recover. 16 U.S.C. § 1539 (a)(1)(B), 2(B). A Section 10 “Incidental Take Permit” (“ITP”) is issued by the USFWS after development and submission of a Habitat Conservation Plan (“HCP”), which must be approved by the USFWS. 16 U.S.C. § 1539 (a)(2)(A); (B). The HCP must include conservation measures designed to minimize and mitigate the impacts of taking species listed under the Act. 16 U.S.C. § 1539 (a)(2)(A)(ii). In the absence of an ITP or other exemption, the ESA forbids each and every take. 16 U.S.C. § 1538 (a)(1).
Recognizing that some human activities will necessarily encroach upon wildlife, and in some instances, involve endangered species, ESA § 10 offers a method by which the developer, applicant or entity works with the USFWS to anticipate the impact of their actions and to minimize the potential take of an endangered species. Here, TAP is asking the Court to order the TCEQ defendants to apply for an ITP, thus acknowledging that their permit process and water enforcement actions, especially in times of drought, alter the critical habitat of the AWB cranes and can lead to a “take” of these endangered birds. Once the ITP is filed, ESA § 10 requires TCEQ defendants to work with the USFWS to formulate a Habitat Conservation Plan based on the best science available.
III. FINDINGS ON STANDING AND JURISDICTION.
A. Standing.
The ESA expressly authorizes citizen suits against any “person” alleged to be responsible for a “take.” The ESA provides that any person may commence a civil suit on his own behalf — (A) to enjoin any person, including the United States *728 and its agencies, who is alleged to be in violation of ESA provisions or regulations; (B) to compel the Secretary to enforce the provisions concerning the taking of any resident endangered species or threatened species within any State; or (C) against the Secretary where there is an alleged failure of the Secretary to perform any nondiscretionary act or duty. 16 U.S.C. § 1540 (g)(1); see also Tennessee Valley Auth., 437 U.S. at 184 , 98 S.Ct. 2279 ; Defenders of Wildlife v. Bernal, 204 F.3d 920, 925 (9th Cir.2000). The district courts shall have jurisdiction, without regard to the amount in controversy or the citizenship of the parties, to enforce any ESA provision or regulation, or to order the Secretary to perform such act or duty, as the case may be. 16 U.S.C. § 1540 (g). Although the ESA provides for citizens suits, the ESA plaintiff must satisfy the jurisdictional requirements of standing. Bennett v. Spear, 520 U.S. 154, 162 , 117 S.Ct. 1154 , 137 L.Ed.2d 281 (1997). To satisfy the “case” or “controversy” requirement of Article III, which is the “irreducible constitutional minimum” of standing, a plaintiff must, demonstrate that he has suffered: injury in fact; that the injury is “fairly traceable” to the actions of the defendant, and that the injury will likely be redressed by a favorable decision. Lujan v. Defenders of Wildlife, 504 U.S. 555, 560-561 , 112 S.Ct. 2130 , 119 L.Ed.2d 351 (1992).
1. Injury in fact.
In this case, the TCEQ defendants, GBRA, and SARA, have consistently challenged TAP’s standing to sue. (See D.E. 213, 214, 215). In its December 5, 2011, 835 F.Supp.2d 251 (S.D.Tex.2011), Order denying TCEQ defendants’ and intervenor’s motion for partial summary judgment (D.E. 270), the Court found that TAP had satisfied the standing elements of injury in fact and redressability. Id. at 258-60 . As to the injury requirement, the Court noted that many of the TAP members reside and work in the Aransas area and, for some, their livelihood depends in large part on the AWB cranes. (D.E. 270, 835 F.Supp.2d at 258-59 ). Indeed, the tourism economy of the area relies on the annual migration of the Whooping Cranes to the nearby Refuge. This finding was reinforced by testimony at trial. For example, TAP member Albert Johnson is the proprietor of The Crane House, a small home that is rented to tourists, photographers, and naturalists that come specifically to observe the Whooping Cranes. 15 (Johnson, Day 4, Tr. 182-183). TAP member Ray Kirkwood works as the narrator on the Wharf Cat, a boat that tours the Aransas Refuge, allowing visitors to observe a healthy, active estuarial system, and the AWB Whooping Cranes in their winter home. (Kirkwod, Day 4, Tr. 136, 141, 146-148). Aransas County Judge Burt Mills testified that the AWB flock has always been an important aspect of the tourist industry for Aransas County. (Mills, Day 4, Tr. 108, 117).
In addition, the Court found that many of TAP’s members are active birders and devote substantial time and effort to observing Whooping Cranes and other birds in their natural habitat. (D.E. 270, 835 F.Supp.2d at 258-59 ). At trial, Deborah Corpora, a Rockport birder, testified as to the pleasures of watching the Whooping Cranes at the Aransas Refuge. (Corpora, Day 3, Tr. 154-170). The evidence was uncontested that TAP members had aesthetic, recreational, economic, professional, and other interests in photographing, studying, protecting and otherwise enjoying the AWB cranes in their natural environment. (D.E. 270, 835 F.Supp.2d at 258-59 ).
*729 The Supreme Court has recognized that “environmental plaintiffs adequately allege injury in fact when they aver that they use the affected area and are persons “for whom the aesthetic and recreational values of the area will be lessened” by the challenged activity.” Friends of the Earth, Inc. v. Laidlaw Envtl. Servs. (TOC), 528 U.S. 167, 183 , 120 S.Ct. 693 , 145 L.Ed.2d 610 (2000). Fewer AWB cranes would adversely affect the tourism, visual observation, and recreational enjoyment of TAP members. Thus, TAP successfully demonstrated that its members were “among the injured” for purposes of standing. Lujan, 504 U.S. at 562-63 , 112 S.Ct. 2130 .
2. Redressability.
In denying TCEQ defendants’ and GBRA’s motion for partial summary judgment, the Court previously found that TAP had also established redressability. (D.E. 270, 835 F.Supp.2d at 259-61 ). To establish redressability, it must be “likely, as opposed to merely speculative, that the injury will be redressed by a favorable decision.” Friends of the Earth, Inc., 528 U.S. at 181 , 120 S.Ct. 693 . The relevant question is simply, “whether a plaintiff personally would benefit in a tangible way from the court’s intervention.” Steel Co. v. Citizens for a Better Environment, 523 U.S. 83 , 103 n. 5, 118 S.Ct. 1003 , 140 L.Ed.2d 210 (1998) (internal quotation marks omitted). “When ... a plaintiffs asserted injury arises from the government’s allegedly unlawful regulation (or lack of regulation) of someone else ... causation and redressability ordinarily hinge on the response of the regulated (or regulable) third party to the government action or inaction-and perhaps on the response of others as well.” Lujan, 504 U.S. at 562 , 112 S.Ct. 2130 .
In their motion for partial summary judgment, and again at trial, the TCEQ defendants argued that they lacked the authority or the power to control the activities of permitted water right users and Domestic and Livestock (D & L) water right owners. (D.E. 214). GBRA argued that, even if the TCEQ defendants did have the authority to alter the issuance of new or existing water permits, such an action would not noticeably affect freshwater flows to the Aransas Refuge such that any ordered relief would be “pointless.” (D.E. 215). The Court rejected those arguments pretrial finding that, based on the summary judgment evidence alone, the TCEQ defendants have the authority over water permits and water diversions. (D.E. 270, 835 F.Supp.2d at 260-61 ). At trial, witnesses for TAP established that the TCEQ defendants have the plenary authority to implement Texas laws and to fulfill federal law, and more particularly, the ESA, 16 and that declaratory and injunctive relief would most certainly help the AWB flock.
With respect to declaratory judgments, the Supreme Court has stated, “the question ... is whether the facts alleged, under all the circumstances, show that there is a substantial controversy between parties having adverse legal interests, or sufficient immediacy and reality to warrant the issuance of a declaratory judgment.” MedImmune, Inc. v. Genentech, Inc., 549 U.S. 118, 127 , 127 S.Ct. 764 , 166 L.Ed.2d 604 (2007). TAP seeks a declaration that the TCEQ defendants have violated ESA Section 9 in the past and are presently violating Section 9 by issuing water permits and authorizing diversions, as well as a declaration that water diversion regulations are preempted by federal law when they pur *730 port to allow activities that result in the taking of Whooping Cranes. (D.E. 1 at 32, ¶¶ A, B, C). Such a declaration would assist TAP in its overall goal of developing a plan to protect the AWB flock. 17
TAP has requested injunctive relief. (D.E. 1 at 32-33, ¶ ¶ D, E). At trial, the Court heard testimony from TCEQ officials including Mark Vickery, a former TCEQ Executive Director, who testified that the TCEQ has the authority to issue or deny a permit, or to impose conditions on the permit. (Vickery, Day 4, Tr. 205). Indeed, the TCEQ has the “continuing right of supervision of State water resources.” Id. Tr. 204. The Court rejects the TCEQ defendants’ arguments that they are essentially powerless to regulate water resources in the manner TAP suggests. An injunction preventing new approvals of permits until there are “sufficient assurances” that these permits will not result in harm to the Whooping Cranes could effectively redress TAP’s concerns regarding freshwater inflows to the Refuge for the benefit of the AWB flock.
Finally, as to TAP’s request for development of an HCP and the issuance of an ITP under 16 U.S.C. § 1539 (a)(2), this too would redress TAP’s injury. The Supreme Court has rejected overly “draconian interpretation[s] of the redressability requirement.” Larson v. Valente, 456 U.S. 228 , 243 n. 15, 102 S.Ct. 1673 , 72 L.Ed.2d 33 (1982). A plaintiff “satisfies the redressability requirement when he shows that a favorable decision will relieve a discrete injury to himself. He need not show that a favorable decision will relieve his every injury.” Id. At trial, TAP’s experts offered several proposals to prevent future takings of Whooping Cranes. TAP has satisfied the standing requirement of redressability.
3. Causation.
As to the third element of standing, causation, the Court found prior to trial a relationship between the TCEQ defendants’ water management practices and the freshwater flows to the Aransas Refuge. (D.E. 270, 835 F.Supp.2d at 261-65 ). However, as to the second aspect of causation in this case, namely, TAP’s allegation that low freshwater flows caused the deaths of at least 23 Whooping Cranes in 2008-2009, the Court concluded that material issues of fact remained. Id. at 264-65 .
The federal courts have found causation where there has been a direct relationship between the challenged government regulation and the resulting “take.” For example, in Loggerhead Turtle v. County Council of Volusia County, plaintiffs sued Volusia County, alleging inter alia, that its refusal to ban beachfront artificial light sources (cars), adversely impacted the loggerhead turtle, resulting in a taking in violation of ESA Section 9. 148 F.3d at 1234-35 . The Eleventh Circuit found the plaintiffs had standing, and had sufficiently alleged causation based upon the lack of regulation, “even though the actions or inactions of those third parties not before the court may be another cause of the harm.” 148 F.3d at 1253 (internal citations and quotation marks omitted). Similarly, in Strahan v. Coxe, the district court found sufficient causation between harm to the endangered northern Right Whale and governmental regulation of commercial fishing vessels and whale-watching vessels in Massachusetts waters. The court explained:
*731 Indisputably, the actions of third parties not before the court — commercial fishing and whale watch operations — are the immediate cause of the harm to endangered whales alleged here. Defendants do not place gillnets and lobster gear in coastal waters, nor do they operate whale watch vessels. Nevertheless, the actions of these third parties are dependent on the actions of the Defendants. Fishing vessels cannot, legally, place gillnets and lobster gear in Massachusetts waters without permission from the Defendants. And whale watch vessels cannot, legally, approach within 500 yards of Right whales in Massachusetts waters without permission from the Defendants. Thus, to the extent that he challenges the operations of licensed commercial fishing and whale watch vessels, Strahan has shown a causal connection between the injury he has suffered (and will continue to suffer) and the actions of the Defendants in issuing such licenses.
Strahan v. Coxe, 939 F.Supp. 963, 978-79 (D.Mass.1996) (emphasis added); see also Defenders of Wildlife v. Gutierrez, 532 F.3d 913, 924 (D.C.Cir.2008) (in suit against Coast Guard alleging violations of ESA Section 9 due to establishment and maintenance of shipping lanes in areas inhabited by right whales, court rejected argument that chain of causation was too attenuated); Seattle Audubon Soc’y v. Sutherland, 2007 WL 1300964 (W.D.Wash. May 1, 2007) (finding sufficient causation between state agency regulation over logging and taking of spotted owls, explaining, “[t]he alleged destruction of spotted owl habitat on private lands is fairly traceable to State Defendants’ actions because State Defendants enforce the rules governing such logging operations and the independent logging operators cannot conduct Class III applications on their private lands without the authorization of the Department.”).
As will be discussed in the Findings below, at trial TAP offered essentially uncontroverted evidence to establish: (1) the TCEQ defendants are responsible for water permitting and water diversions from the San Antonio and Guadalupe River systems, and the increased water diversions have left less water for the cranes; (2) reduced water flows lead to high bay/estuary salinities (in excess of 30 to 40 ppt in wide spread sampling); (3) high San Antonio bay/Guadalupe estuary salinities lead to a reduction in the availability of wolfberries, blue crabs, and fresh drinking water; (4) the reduced availability of the cranes’ primary food sources, coupled with the expenditure of more energy to fly farther to search for food and freshwater, leads to malnourishment and death; and (5) TCEQ defendant’s water practices caused the death of at least 23 whooping cranes in the 2008-2009 winter. That is, the mortality of the Whooping Crane population is directly attributable to the lack of freshwater inflows to these crucian estuaries.
B. Burford abstention.
In both their pre- and post-trial briefings, defendants and intervenors have requested that the Court abstain from adjudicating this case pursuant to the Supreme Court’s holding in Burford v. Sun Oil Co., 319 U.S. 315 , 63 S.Ct. 1098 , 87 L.Ed. 1424 (1943) (“Burford abstention”).
In Burford , the Supreme Court affirmed a district court decision dismissing an action in which the Sun Oil Company challenged a Texas Railroad Commission order granting Burford a permit to drill certain oil wells. 319 U.S. at 316-17 , 63 S.Ct. 1098 . The competing drilling interests plus the State’s regulatory powers of oil and gas conservation all came into play. Id. at 318 , 63 S.Ct. 1098 . Recognizing the significant state regulatory framework, the Court concluded that federal court abstention was proper. The Court reasoned:
*732 The state provides a unified method for the formation of policy and determination of cases by the Commission and by the state courts. The judicial review of the Commission’s decisions in the state courts is expeditious and adequate. Conflicts in the interpretation of state law, dangerous to the success of state policies, are almost certain to result from the intervention of the lower federal courts. On the other hand, - if the state procedure is followed from the Commission to the State Supreme Court, ultimate review of the federal questions is fully preserved here. Under such circumstances, a sound respect for the independence of state action requires the federal equity court to stay its hand.
Bwrford, 319 U.S. at 333-34 , 63 S.Ct. 1098 .
The Fifth Circuit has explained that, “Burford abstention applies when a case involves a complex issue of unsettled state law that is better resolved through a state’s regulatory scheme.” Moore v. State Farm Fire & Cas. Co., 556 F.3d 264, 272 (5th Cir.2009) (citing Burford v. Sun Oil Co., 319 U.S. 315, 332 , 63 S.Ct. 1098 , 87 L.Ed. 1424 (1943)). As part of its Bwrford abstention analysis, a court must consider five factors: (1) whether the cause of action arises under federal or state law; (2) whether the case requires inquiry into unsettled issues of state law or into local facts; (3) the importance of the state interest involved; (4) the state’s need for a coherent policy in that area; and (5) the presence of a special state forum for judicial review. Moore v. State Farm Fire & Cas. Co., 556 F.3d 264, 272 (5th Cir.2009) (citing Wilson v. Valley Elec. Membership Corp., 8 F.3d 311, 314 (5th Cir.1993)).
Burford abstention represents “an extraordinarily and narrow exception to the duty of the District Court to adjudicate a controversy properly before it.” Quackenbush v. Allstate Ins. Co., 517 U.S. 706, 727-28 , 116 S.Ct. 1712 , 135 L.Ed.2d 1 (1996); Wilson v. Valley Elec. Membership Corp., 8 F.3d 311, 313 (5th Cir.1993) (explaining that abstention remains the exception, not the rule). The “federal courts’ obligation to adjudicate claims within their jurisdiction [is] virtually unflagging.” New Orleans Public Serv., Inc. v. Council of City of New Orleans, (“NOPSI"), 491 U.S. 350, 359 , 109 S.Ct. 2506 , 105 L.Ed.2d 298 (1989).
The most important aspect of Bwrford is whether there exists a state process to which a federal court might abstain. That is, there must be “time and adequate state-court review” available. NOPSI, 491 U.S. at 360 , 109 S.Ct. 2506 . Additionally, the NOPSI court underscored “[w]hile Burford is concerned with protecting complex state administrative processes from undue federal interference, it does not require abstention whenever there exists such a process, or even in all cases where there is ‘potential for conflict’ with state regulatory law or policy.” Id. at 362 , 109 S.Ct. 2506 (quoting Colorado River Water Conservation District v. United States, 424 U.S. 800, 815-16 , 96 S.Ct. 1236 , 47 L.Ed.2d 483 (1976)).
In arguing for abstention, defendants and intervenors rely on the Fifth Circuit’s decision in Sierra Club v. City of San Antonio, 112 F.3d 789 (5th Cir.1997), an ESA case involving water withdrawals from the Edwards Aquifer that affected an endangered species, the fountain darter. Id. at 791 . The district court issued an ESA injunction ordering the water officials to limit pumping from the Edwards Aquifer based on spring flows. 18 Id. The in *733 junction was to remain in effect until the defendants demonstrated a water management plan that would preserve the fountain darter, and defendants were further ordered to supply the court and a special master with monthly water usage information. Id. On appeal, the Fifth Circuit held that the lower court erred by issuing an injunction finding that the case was not likely to succeed on the merits due to Burford . The Fifth Circuit noted the need for “uniform regulation” in the state regime governing water withdrawals, and found that the legislation in place, the “Edwards Aquifer Act,” could “fairly be characterized as a comprehensive regulatory scheme. It represents a sweeping effort by the Texas Legislature to regulate the aquifer with due regard for all competing demands for the aquifer’s water.” Sierra Club, 112 F.3d at 794 .
1. Senate Bill 3.
The TCEQ defendants, GBRA, and SARA argue that abstention is warranted in this case because the State of Texas now has in place a comprehensive regulatory scheme, Senate Bill 3 (S.B.3), that regulates the State’s surface water flows. See Tex. Water Code § 11.1471, Environmental Flow Standards and Set-Asides (2007). The TCEQ and GBRA argue that S.B.3 addresses a number of environmental issues, including endangered species, and attempts to present a comprehensive state regulatory scheme such that federal abstention is mandated. TCEQ defendants and GBRA maintain that federal intervention would disrupt the S.B.3 process and undermine the State’s efforts to manage its surface waters.
In 2001, the 77th Texas legislature passed Senate Bill 2, which directed the TCEQ, the Texas Water Development Board (TWDB), and the Texas Parks and Wildlife Department (TPWD), in cooperation with other agencies, “to ... jointly establish and continuously maintain an in-stream flow data collection and evaluation program.” Texas Water Code (TWC) § 16.059. In addition, the agencies were directed to “... conduct studies and analyses to determine appropriate methodologies for determining flow conditions in the state rivers and streams necessary to support a sound ecological environment.” Id.
In 2007, the Texas legislature passed S.B.3, establishing the Environmental Flows Allocation Process, also known as “E-flows,” to address inflow water needs. See TWC § 11.1471 et seq. S.B.3 mandates that the TCEQ:
(1) adopt appropriate environmental flow standards for each river basin and bay system in this state that are adequate to support a sound ecological environment, to the maximum extent reasonable considering other public interests and other relevant factors;
(2) establish an amount of unappropriated water, if available, to be set aside to satisfy the environmental flow standards to the maximum extent reasonable when considering human water needs; and
(3) establish procedures for implementing an adjustment of the conditions included in a permit or an amended water right ...
TWC § 11.1471(a). To achieve these objectives, S.B.3 directs the TCEQ to establish and implement a comprehensive plan for each of Texas’ seven major river basins and bays to determine appropriate E-flows.
Pursuant to S.B.3, the TCEQ developed a scheme for collecting data and information to formulate E-flow recommendations. TWC § 11.02362 et seq. For each river .basin and bay system, there is a stakehold *734 er team and a science team to consider and formulate flow recommendations to the TCEQ, and there are two statewide groups that oversee the entire process. 19 The statewide Environmental Flows Advisory Group (EFAG) is responsible for appointing members to the statewide Science Advisory Committee, as, well as appointing members to each local stakeholder team. 20 TWC § 11.0236. EFAG is permitted to make comments on the recommendations of the local science teams for each basin. Id.
The Science Advisory Committee (SAC) is responsible for defining the geographical extent of each river basin and bay system for the “sole purpose of developing environmental flow regime recommendations.” TWC § 11.02361. The SAC provides overall direction and coordination, and ensures that consistent and acceptable scientific principles are utilized throughout the environmental flows allocation process in each region. The SAC has issued technical guidance documents for the local science teams to use in developing recommended flow regimes, 21 and has created a framework for review and evaluation of the science team recommendations. 22
Under S.B.3, each region has a Basin and Bay Area Stakeholder Committee (BBASC). TWX § 11.02362(c)(1). The BBASC stakeholder team for each region must have at least seventeen members, and these teams are required to reflect a fair and equitable balance of local groups with interests in the basin and bay system. 23 The stakeholder team considers the recommendations of the science team, but it also considers other factors, including the present and future water needs related to water supply planning for that local basin and bay system. The BBASC is charged with appointing members to the area’s Basin and Bay Expert Science Team (“BBEST”). TWC § 11.02362(c)(3). BBEST members are required to be technical experts with special knowledge regarding the river basin and bay system or the development of environmental flow regimes. TWC § 11.02362®, (m). Pursuant to S.B.3, the local BBEST science team calculates the amount of water that needs to remain instream to protect the health and vitality of the given estuary. The BBEST submits its recommendations to the stakeholder BBASC team, as well as to the TCEQ. The stakeholder team consid *735 ers the BBEST’s recommended environmental flow regime, adds their associated policy considerations, and develops strategies to meet the flow recommendations. TWC § 11.02362(0). BBASC is not, however, required to follow or give any particular weight to the BBEST’s technical recommendations. (Montagna, Day 3, Tr. 232-33). The implementation strategies for protecting flows can include options such as efficiency incentives, the dedication of treated wastewater, and the purchase or donation of existing water rights. Id.
After the BBEST and BBASC each make a recommendation to the TCEQ, the TCEQ, through a public rule-making process, has one year to use those recommendations to legally adopt environmental flow standards for the river basin and inflows to the associated bay system. 24
Although S.B.3 does establish a comprehensive framework for the State of Texas to determine the amount of freshwater inflows that need to remain instream to protect the overall health of the State’s river system, it makes no attempt to ensure that such recommended amounts remain. Indeed, to the contrary, S.B.3 specifically excludes from consideration the inflow needs of the bays and estuaries in times of water shortages. In addition, S.B.3 fails to address existing permits and water usage. In short, S.B.3 does not address, concern, protect, or assist the endangered whooping cranes, and therefore, provides no grounds for abstention.
S.B.3 sets forth the “Policy Regarding Waters of the State.” TWC § 11.0235. It recognizes that the waters of the state are held in trust for the public, and that the right to use state water may be appropriated only as expressly authorized by law. Id. § 11.0235(a). It acknowledges that maintaining the biological soundness of the state’s rivers, lakes, bays, and estuaries “is of great importance to the public’s economic health and general well-being,” and it encourages “voluntary water and land stewardship to benefit the water in the state, ...”. TWC § 11.0235(b). However, there is no steadfast commitment to the bays and estuaries:
The legislature has expressly required the [TCEQ] commission while balancing all other public interests to consider and, to the extent practicable, provide for the freshwater inflows and instream flows necessary to maintain the vitality of the state’s streams, rivers, and bay and estuary systems in the commission’s regular granting of permits for the use of state waters. 25
TWC § 11.0235(c) (emphasis added). Thus, consideration of the bays and estuar *736 ies is initially relegated “to the extent practicable” status in balancing water demands. But to add insult to injury, the legislature goes on to provide that, in times of water shortages and drought, the needs of the bays and estuaries are expressly exempt from consideration:
... As an essential part of the state’s environmental flows policy, all permit conditions relating to freshwater inflows to affected bays and estuaries and in-stream flow needs must be subject to a temporary suspension if necessary for water to be applied to essential beneficial uses during emergencies.
TWC § 11.0235(d). That is, in times of drought or other water emergencies, S.B.3 specifically authorizes the TCEQ to suspend the recommended freshwater inflows to bays and estuaries that the S.B.3 process had determined to be necessary to maintain the ecosystem’s health.
Under S.B.3, “beneficial use” is defined as the “use of the amount of water which is economically necessary for a purpose authorized by this chapter, when reasonable intelligence and reasonable diligence are used in applying the water to that purpose and shall include conserved water.” TWC § 11.001(4). S.B.3 specifically identifies
numerous purposes for which water may be appropriated. TWC § 11.023(a). This list includes domestic and municipal uses; agricultural and industrial use, including development of power by means other than hydroelectric; mining and recovery of minerals; hydroelectric power; navigation; recreation and pleasure; public parks; and game preserves. Id. § 11.023(a)(1), (2). The water needs of whooping cranes and other endangered species are not addressed by S.B.3, and in times of drought, they are expressly disregarded.
Moreover, the Texas legislature has specifically excluded as a beneficial use the allowance of water instream to benefit a bay or estuary. In response to state court litigation in which applicants sought a permitted water right to leave water in-stream, 26 the Texas legislature passed § 11.0237(a) of the Texas Water Code, which provides:
The commission may not issue a new permit for instream flows dedicated to environmental needs or bay and estuary inflows. The commission may approve an application to amend an existing permit or certificate of adjudication to change the use to or add a use for instream flows dedicated to environmental needs or bay and estuary inflows.
TWC § 11.0237(a). Thus, Texas law prohibits the TCEQ from issuing a water permit for the purpose of allowing water to remain instream to maintain the bay or estuary inflows, or to otherwise address environmental needs.
Finally, S.B.3 does not assist the whooping cranes because it applies only to applications for new water permits; it does not attempt to modify or amend water rights with priority dates earlier than September *737 1, 2007. Indeed, S.B.3 expressly prevents use of the E-flow process to regulate water users unless they are seeking new permits or new increases under existing permits:
(1) water appropriated under a permit for a new appropriation of water the application for which is pending with the Texas Commission on Environmental Quality on the effective date of this Act or is filed with the commission on or after that date; or
(2) the increase in the amount of water authorized to be stored, taken, or diverted under an amendment to the existing water right that increases the amount of water to be stored, taken or diverted and the application for which is pending with the Texas Commission on Environmental Quality on the effective date of this Act or is filed with the commission on or after that date.
Section 1.27 of Acts 2007, 80th Leg., ch. 1430 2007 Tex. Gen. Laws 5846 (not codified in the Water Code) (emphasis added). Thus, S.B.3 and its quasi-considerations of maintaining necessary inflows has no impact on existing permits with a priority date before September 1, 2007. In addition, until the staggered S.B.3 process is actually completed, the TCEQ can continue to issue new water permits without regards to inflows. 27
S.B.3 establishes an administrative scheme to determine freshwater inflows to the state’s bays and estuaries. It does not provide for enforcement of those recommendations, nor provide for penalties if the recommended inflows are not maintained. In addition, S.B.3 set certain deadlines for flow determinations to be made and adopted, but to date, no region has suceessfully completed the E-flow process. The TCEQ defendants, as well as GBRA and SARA, argue that S.B.3 provides an elaborate regulatory scheme for environmental flows that will address the concerns of the Whooping Crane, that federal intervention would disrupt the E-flow process, and therefore, that abstention is mandated under Burford . The Court disagrees. The mere existence of a state-created administrative body does not override the jurisdictional power of a federal court. The E-flow scheme and process may hopefully provide important and scientifically sound information to water officials and policy makers concerning each basin and bay, and eventually, promote actions to secure the recommended inflows and keep the rivers “wet.” However, to suggest that S.B.3 can protect the whooping cranes, when by its own admission, it specifically excludes the cranes’ habitat in times of water emergencies, is to argue that state law preempts federal law. This topsy-turvy view of federalism and the Constitution’s Supremacy Clause has no basis in the existing constitutional scheme. The Court has jurisdiction under the ESA.
2. Texas surface waters.
Moreover, the Court finds that, not only does the ESA mandate federal court intervention in this case, but Texas’ own water laws and policies warrant judicial oversight in this instance because, contrary to the position of defendants and intervenors, Texas law specifically authorizes the TCEQ to manage the State’s surface waters in a manner consistent with conservation and in compliance with federal law, and the TCEQ defendants have failed to do so.
*738 The surface waters in the State of Texas are owned by the state itself:
(a) The water of the ordinary flow, underflow, and tides of every flowing river, natural stream, and lake, and of every bay or arm of the Gulf of Mexico, and the storm water, floodwater and rainwater of every river, natural stream, canyon, ravine, depression, and watershed in the state is the property of the state.
(b) Water imported from any source outside the boundaries of the state for use in the state and which is transported through the beds and banks of any navigable stream within the state or by utilizing any facilities owned by the state is property of the state.
TWC § 11.021.
“The waters of the state are held in trust for the public.” TWC § 11.0235(a). No person may divert, store or impound state-owned water without authorization, by permit, certificate of adjudication, or one of the statutory exemptions. 28 TWC §§ 11.081,11.121.
Some water rights, such as Domestic and Livestock (D & L), are exempt from the permitting or adjudication process. 29 TWC § 11.142. A D & L user may divert water from a stream or may impound up to 200 acre-feet 30 of water at a time in an impoundment or reservoir. 31 Id. D & L water rights are not recorded, nor are they monitored by any water enforcement office. (Soward, Day 4, Tr. 253).
The TCEQ is the state agency with “general jurisdiction” over both “water and water rights” in Texas. 32 TWC § 5.013(a). *739 Via statute, the Texas legislature has conferred upon the TCEQ the plenary authority to implement Texas laws and to fulfill federal law. TWC § 5.015. The Texas Supreme Court has held that, when the legislature confers agency power, it impliedly intends that the agency have whatever powers are reasonably necessary to fulfill its express functions or duties. Texas Natural Res. Conservation Comm’n v. Lakeshore Util. Co., 164 S.W.3d 368, 377-78 (Tex.2005). 33
Texas’ legal framework for resolving water conflicts is based on permit priority. Section 11.027 of the Texas Water Code provides simply: “As between appropriators, the first in time is the first in right.” TWC § 11.027.
Former and current TCEQ employees and officials testified at trial about their water management responsibilities and powers. A1 Segovia is a named TCEQ defendant in this action, and at the time this suit was filed, he was employed as both the South Texas Watermaster and the Concho River Watermaster. (Segovia, Day 4, Tr. 52). In certain river basins, the TCEQ has implemented a watermaster program to protect priority water uses. See TWC § 11.326. The purpose of the watermaster program is to manage, monitor, archive, and enforce surface water rights based on priority. Id. Tr. 53-54.
Under the watermaster program, water right owners, junior and senior, must contact the watermaster before diverting water. Id. Tr. 55. Depending on the river conditions at the time, the watermaster can grant permission, delay permission, or if necessary due to drought, deny permission to take water. Id. The watermaster keeps records and monitors water use of permitted water right owners through various reporting mechanisms and forms. 34 Id. Tr. 57.
Water rights are relative to one another; the oldest water right is the most senior, and all other rights are junior to it. (Segovia, Day 4, Tr. 60). If a junior water right owner seeks to withdraw water during a drought, the watermaster must organize a meeting to discuss the situation and determine if other owners can reduce their use. Id. Tr. 61. In reality, the watermaster program is “no more than a balancing act,” and it presents “a constant battle.” Id. The watermaster has the authority to tell a water owner: “You can’t take this water at this time.” Id. Indeed, water users are “all under the same drought.” Id.
When water diversions must be reduced, junior right holders are restricted first. (Segovia, Day 4, Tr. 62). However, because Texas often suffers from drought conditions, even senior holders must be *740 restricted at times, and the watermaster has the authority to order restrictions or limitations on the amount of water diverted. Id. Tr. 70-71. The first priority owners are those with D & L/riparian rights, and it is the watermaster’s job to ensure that downstream riparian right owners get their water. Id. Tr. 71. One method to address water demand is to stagger use along the river. Id. at 62. The primary objective is to “keep the river wet.” Id.
D & L/riparian right owners are authorized to withdraw 200 acre-feet of water annually. (Segovia, Day 4, Tr. 77-79). And see TWC § 11.142. However, the watermaster does not monitor the D & L/riparian owner’s use. Id. A watermaster might visually check stored water to see if it remains at the same capacity, but there is no way of determining whether the riparian owner emptied and refilled the reservoir, thus using more than the allowed 200 acre-feet. Id. Tr. 78-79.
Recently retired TCEQ Executive Director Mark Vickery, a named defendant in his official capacity, testified for TAP about the TCEQ’s administrative and monitoring responsibilities concerning permitted water withdrawals, as well as enforcement authority. (Vickery, Day 4, Tr. 195). In his role as Executive Director, he had policy discretion, as well as implementation authority. Id. Tr. 198.
The TCEQ has enforcement authority over certificates of adjudication and water permits, and it has the authority to issue or deny a permit with conditions. (Vickery, Day 4, Tr. 205). The TCEQ has the authority to contact industries about their water use and to encourage conservation efforts, such as industrial recycling. 35 Id. Tr. 210-211. Some permits require return flows, but it is not “routine, and most older permits do not include a return flow requirement.” Id. Tr. 212.
The Oath of Office for TCEQ Commissioners requires them to comply with federal law. 36 (Vickery, Day 4, Tr. 212, 215). Since 1985, the water permit process now requires the TCEQ to consider the impact of water diversions on bays and estuaries. Id. Tr. 218. And see TWC § 11.147(b). In addition, effective September 1, 2011, the legislature enacted section 11.053(c) of the Texas Water Code, entitled EMERGENCY ORDER CONCERNING WATER RIGHTS, which provides, in part:
(a) During a period of drought or other emergency shortage of water, as defined by commission rule, the executive director by order may, in accordance with the priority of rights established by Section 11.027:
(1) temporarily suspend the right of any person who holds a water right to use the water; and
(2) temporarily adjust the diversions of water by water rights holders.
(b) The executive director in ordering a suspension or adjustment under this section shall ensure that an action taken:
(1) maximizes the beneficial use of water;
(2) minimizes the impact on water rights holders;
(3) prevents the waste of water;
(4) takes into consideration the efforts of the affected water rights holders to develop and implement the water conservation plans and drought contingency plans required by this chapter;
*741 (5) does not require the release of water that, at the time the order is issued, is lawfully stored in a reservoir under water rights associated with that reservoir.
TWC § 11.053.
Mr. Vickery agreed that, pursuant to the § 11.053 emergency rule, the TCEQ now expressly has the authority to suspend or adjust water diversions in times of drought. Id. Tr. 217. The TCEQ is charged with adopting rules to implement this section. Id.
The TCEQ has the discretion to make exceptions in both enforcement and in the implementation of terms and conditions of water rights. (Vickery, Day 4, Tr. 224). For example, in 2008-2009, the TCEQ accommodated a request from the City of Kerrville to withdraw water to ensure that the public’s health was protected. Id. The City of Kerrville was a junior water right. Id.
Mr. Larry Soward is a retired public servant with first-hand knowledge of not only the TCEQ, but its predecessor agencies, as well as state departments in land and agriculture. 37 (Soward, Day 4, Tr. 235). His testimony established that the TCEQ has authority “across the board,” in times of drought, and it can “... issue an emergency order to basically do anything that is necessary or appropriate to carry out their duties and responsibilities ..., in an emergency situation.” (Soward, Day 4, Tr. 266). In Mr. Soward’s opinion, the TCEQ could use its emergency powers to protect the bays, estuaries, and whooping cranes. Id. S.B.3 does not provide protection to the cranes. Id. To the contrary, S.B.3 authorizes the TCEQ to suspend the recommended inflow provisions during times when the flow is not sufficient to meet the needs of water right holders. Id. S.B.3 expressly allows for bays and estuaries to be left unprotected in times of “emergencies,” that is, drought, the very time when the cranes need those inflows to be maintained. Id. Tr. 268.
There are a number of methods available to the TCEQ to evaluate and address the competing demands for water. (So-ward, Day 4, Tr. 274-275). Under its emergency powers, the TCEQ can modify the usufructory rights of permit holders. Id. Tr. 270. With the September 1, 2011 enactment of TWC § 11.053, the TCEQ now has the express authority to suspend or adjust water diversions in times of drought. Id. Thus, the TCEQ is no longer constrained by “first in time, first in right.” Id. Tr. 271. The threatening of an endangered species could constitute an “emergency” or fall under the “public welfare” provision of § 11.053. Id. Tr. 271-272.
Finally, Mr. Vickery noted that there is no prohibition to prevent the TCEQ from requiring an inventory of D & L users. Id. The TCEQ could initiate surveys to determine how currently permitted water is being used and initiate cancellation of unused water rights. Id. In addition, although the TCEQ does not require used water to be returned to the stream, it is required by statute, and the TCEQ could enforce water return. Id. Tr. 275.
TAP’s witnesses established that the TCEQ has the authority to modify or amend existing water rights, delay or deny issuance of new permits, access and evaluate D & L usage, and take any other action necessary in times of emergencies, including drought, to ensure that the necessary freshwater inflows reach the Aransas Refuge and the AWB cranes. Despite this authority, the TCEQ defendants did not exercise it in 2008-2009, and the permitted water diversions, along with the *742 drought, effectively choked the San Antonio bay/Guadalupe estuary, creating hyper-saline conditions and adversely affecting the health of the AWB cranes.
In rebuttal to TAP’s witnesses on TCEQ authority, the TCEQ defendants offered Mr. Todd Chenoweth, TCEQ special counsel for the Office of Water. 38 (Chenoweth, Day 5, Tr. 147-148). Mr. Chenoweth reiterated TAP witnesses’ testimony concerning the water permit process and provided additional detail in some areas. He did not contradict or dispute TAP’s allegations that the TCEQ has authority to manage permitted water rights or address D & L usage. In fact, Mr. Chenoweth affirmed TCEQ’s broad authority to manage water resources, and speculated as to additional actions the TCEQ could take under its broad powers. As previously noted, the TCEQ’s duty to consider the water needs of the bays and estuaries applies only to those water permits/applications to divert or store water within 200 river miles of the coast. See TWC § 11.147(b). There are no provisions in S.B.3’s E-flow process to extend the range of consideration. (Chenoweth, Day 5, Tr. 163-164). Thus, even with S.B.3, the TCEQ need not consider the impact of freshwater diversions as to any permit application to store or divert water that is outside the 200 river miles from the coast. Many of the lakes and reservoirs that supply the San Antonio bay/Guadalupe estuary are outside of this 200 river miles limit. 39 In fact, the San Antonio River is 240 river miles long and the Guadalupe River 250 miles long. For example, with permit applications, the TCEQ could authorize less water than the amount requested. (Chenoweth, Day 5, Tr. 182). The TCEQ could impose “special restrictions,” prohibiting diversions if the instream water flow rate fell below a certain cubic feet per second (efs). Id. He acknowledged that the TCEQ’s Water Availability Model (WAM) does not take into account exempt D & L users. 40 Id. Mr. Chenoweth proposed other means by which the TCEQ and a water right holder could work together to conserve water use to benefit the environment. 41 That is, Mr. *743 Chenoweth’s testimony confirmed the testimony of TAP’s -witnesses, that the TCEQ has the authority and power to modify, amend, adjust, or in any manner affect priority water rights if it determines it is necessary to do so.
The last witness to testify about TCEQ authority was Margaret Hoffman, an attorney who worked at the TCEQ from 1993 to 2004, and served as the TCEQ executive director for some portion of her time there. 42 (Hoffman, Day 8, Tr. 218-251). Ms. Hoffman testified that TCEQ is constrained by what she called “permanent water rights.” 43 Id. Tr. 232. She explained that a permanent water right is a vested property right, as opposed to term permits, temporary permits, and seasonal permits, that are subject to being cancelled or revisited. Id. Tr. 232. In times of water shortage, those “temporary” rights are modified first. Id.
Ms. Hoffman testified that the Texas Water Code affords highest priority for municipal and domestic use, 44 but that in times of shortage, the TCEQ’s primary responsibility is to protect senior water rights. Id. Tr. 233. Ms. Hoffman was unaware of the September 1, 2011 Emergency Rule, TWC § 11.053, that expressly authorizes the TCEQ to temporarily suspend or adjust the right of any person who holds a water right. Id. Tr. 243-44. She agreed that the TCEQ has the authority to cancel unused water rights, and was unaware of any prohibition against requiring D & L users to report their usage. Id. Tr. 245.
Ms. Hoffman confirmed that the TCEQ could cancel unused water rights, and require D & L users to report their water usage. Because she was unaware of TWC § 11.053, the Emergency Order Concerning Water Rights, effective September 1, 2011, that is, three months prior to trial, she was unable to offer any opinion or testimony as to its scope or application.
The Court concludes that TAP has established by a preponderance of the evidence, that the TCEQ defendants have the authority, power, and responsibility to manage water diversions, and the ESA requires that such management take into account the health and survival of the AWB whooping cranes. The Court finds further that TCEQ has refused to issue a permit to permit freshwater inflow for the protection of the AWB habitat and that S.B.3 either by definition or application will not protect the winter habitat of the AWB.
In summary, S.B.3 does not constitute an elaborate regulatory scheme for environmental flows that will address the concerns of the Whooping Cranes because: (i) it is riddled with carve-outs and exceptions that relegate the ecological needs of the Whooping Cranes’ to a secondary status; (ii) it has no enforcement mechanism, that *744 policy framework, no matter how elaborate, has no “teeth;” (iii) bays and estuaries, in particular, are relegated to a lesser status as, by statute, the TCEQ may not issue a new permit dedicated to the environmental needs of a bay or estuary; and (iv) S.B.3 and its E-flows scheme only applies to the issuing of new water rights or the expansion of an existing water right.
IV. FINDINGS ON CAUSATION.
A. Court’s findings as to witness expertise and credibility.
At trial, TAP presented seventeen (17) witnesses, ten (10) of whom were experts; GBRA eight (8); SARA one (1); and TCEQ two (2). As will be discussed in more detail later, TAP’s experts were world renowned in their respective fields. Several of TAP’s witnesses hold endowed chairs at prestigious universities, some are MacArthur Fellows, all have published numerous scientific papers in respected journals. Indeed, one witness, Dr. Ronald Sass, is a shared recipient of the 2007 Nobel Peace Prize for his environmental work. TAP’s crane experts, Dr. Chavez-Ramirez, Dr. Archibald, and Mr. Stehn, have years of study in the field and have devoted their time and energies to the survival of the AWB species. All of TAP’s experts were accepted as such and the Court finds their testimonies compelling and credible.
In contrast, the Court found an alarming trend in the experts that GBRA offered, most of whom had limited experience and insignificant knowledge of whooping cranes in particular. Indeed, in most instances it was established that GBRA selected the data for which its experts were to make a determination without regard to the peer reviewed published scientific data available. In particular, intervenors GBRA and SARA wholly financed what is called the SAGES report partially designed by Dr. Stephen E. Davis, who testified as a modeling expert, and Dr. R. Douglas Slack. This report did not include the Chavez-Ramirez or Stehn research. In fact, it used a report by Dr. Slack’s graduate student Danielle Greer whose conclusions to the preferred food of whooping cranes was based on 90 plus hours of video of three crane areas. The Court watched all the videos and finds that they were either too blurred to see anything or non-demonstrative of any habit, feeding or otherwise. When subjected to peer review Greer’s conclusions were soundly criticized.
Dr. Slack testified that the whooping cranes had well developed supraorbital salt glands which rid the body of excess salt, making them capable of living in a salt water marsh with no freshwater. When pressed by the Court, he admitted that he had made up that entire statement.
Samuel Vaugh, an engineer who was employed by HDR Engineering in Austin, who has as principal clients GBRA and SARA, was offered as some type of an expert on crane mortality based on faulty information supplied solely by GBRA. GBRA witness, Dr. Miller, admittedly without any evidence to support the testimony stated that decreased blue crab population may be related to commercial fishing. Dr. Porter, GBRA’s “niche mapper,” used mapping based on the diet of the Whooping Crane supplied solely by the SAGES report as found by Greer. Again, this was all that was supplied to him as a “niche mapper” to the exclusion of all other published articles on Whooping Crane diet. Dr. Conroy was offered to challenge the Stehn mortality rates but was completely lacking in any expertise on whooping cranes or their habitat. His testimony relied solely on a prior review of the literature selected and provided by GBRA.
Dr. Stroud, a veterinary pathologist, was offered to explain the Whooping *745 Crane necropsy findings of another pathologist. His opinion was that the carcass that showed an infection was not based on the original pathologist description but based on the original pathologist description that green fluid was observed in a joint. To him the color green meant gangrene. This conclusion had no scientific merit but he kept insisting that when he saw green he thought of gangrene.
In conclusion, these witnesses, offered by GBRA, were not credible and not reliable. A more in depth discussion follows herein.
B. TCEQ’s water diversions reduce freshwater inflows to the Refuge.
TAP argues that lower freshwater inflows to the Refuge from the San Antonio and Guadalupe river systems result in higher bay/estuary salinities, and that the water practices of the TCEQ defendants cause those lower freshwater inflows to the Refuge. For 2008-2009, TAP maintains that those water practices caused the death of at least 23 Whooping Cranes. The fact that those diversions were “lawful water diversions under preexisting permits” is irrelevant in the context of this case because, as previously discussed, the ESA preempts state law to the extent it authorizes activities that cause a prohibited take of a listed species. 16 U.S.C. § 1539 (a)(1)(B).
1. Trungale established permitted water diversions lower inflows to Refuge.
TAP introduced Joe Trungale, a licensed water resources engineer who currently is employed as a private consultant in the Austin area, 45 to demonstrate that TCEQ’s regulation of water causes reduced freshwater inflow to the Refuge, (Trungale, Day 3, Tr. 252). Between 1999 and 2004, Mr. Trungale worked as a river studies hydrologist with the Texas Parks and Wildlife Department. Id. Tr. 253.
Mr. Trungale employed simulation modeling of the San Antonio bay/Guadalupe estuary to predict salinity gradients that would occur in response to different freshwater inflow regimes. (Trungle, Day 3, Tr. 254). The simulation modeling relied upon state and federal data sources, and employed TxBlend, a modeling system developed by the Texas Water Development Board (“TWDB”), 46 and used also by the TCEQ BBEST teams in the major estuary systems along the Texas coast in response to S.B.3. Id. Tr. 254-255. Mr. Trungale has employed the TxBlend model to evaluate salinity in the past and as a member of BBEST teams for Galveston Bay, Matagorda Bay, and the Colorado and Lavaca River basins. Id. Tr. 256-258.
The TxBlend model uses the instream flow data that has been measured by the USGS gauges over time, collected at the three most downstream gauges. (Trungale, Day 3, Tr. 258). Id. These downstream gauges are used because they already reflect the upstream water diversions. Id. Tr. 258. The model includes actual daily data inflow numbers collected from 1988 through 2009. Id. Tr. 261. The gauges are positioned to get the best reflection as to what amount of water is making it from upstream to the mouth of the bay. Id. Tr. 262. Thus, Trungale relied on actual water diversion data as reported to the South Texas Watermaster and TCEQ See DX-300 (list of all Guadalupe River Basin water right owners, permitted and adjudicated); DX-301 (list of all San An *746 tonio River Basin water rights); DX-302 and DX-303 (over 1,000 pages of TCEQ historical data); DX-304 (TCEQ historical use data); and PX-83 (map of water rights in the Guadalupe and San Antonio river basins).
Using these sources of information, Mr. Trungale employed the TxBlend model to generate three different scenarios of freshwater inflows to the San Antonio bay/Guadalupe estuary. 47 TAP’s exhibits PX-92, PX-93, and PX-94, are maps constructed for the time period of May 2008 through April 2009, using the historical data provided. (Trungale, Day 4, Tr. 7). All three exhibits show the salinity patterns in the AWB critical habitat. Id. PX-93 shows the actual salinities in the critical habitat for May 2008-April 2009. Id. PX-92 shows what the salinities would have been if every reported diversion was added back into the stream. Id. Tr. 8. That is, what the salinities would have been if there were no permitted diversions anywhere in the basin and all the river water flowed into the San Antonio bay/Guadalupe estuary. Id. Tr. 9. The third scenario modeled the full use of certain existing permits: it took actual gauged flows and then assumed that six actual lower basin permits (all of which are GBRA’s) diverted water to the maximum amount permitted. Id.; PX-94. Under the “full use of permits” scenario, there are dramatic changes with resulting salinity greater than 25 ppt. Id. Tr. 10. The third scenario reflected a realistic, but very conservative, picture of increased water use in the near future. Id.
Using TWBD inflow data for the full period of record, 1987-2009, TAP exhibit PX-90 was created; it provides a visual representation of the averaged over-time salinity levels across the San Antonio bay/Guadalupe estuary, which of course, includes the Refuge. (Trungale, Day 4, Tr. 10). PX-90 demonstrates that for 2008- 2009, a significant area of the bay had salinities greater than 25 parts ppt. 48 Id. Tr. 12. Coincidentally, the winters of low freshwater inflows and high bay salinities correspond with the other “bad” winter years for cranes: the three winters of 1988-1989, 1989-1990 and 1990-1991 were all years of high winter Whooping Crane mortality (4.3%, 3.4% and 7.8% respectively). See PX-74. That is, as was later confirmed by TAP experts Sass and Ensor, higher salinity years correspond with higher crane mortality. Id.
Low freshwater inflows result in markedly higher salinities in the bays; however, even high salinities in the bay may be rapidly lowered by a month of relatively high freshwater inflows (e.g., October 2009- November 2009). (Trungale, Day 4, Tr. 14); PX-96. For example, in the fall of 2009, at the start of the 2009-2010 Whooping Crane winter season, the bays had lower salinities due to increased inflows. Id. That is, relatively small amounts of freshwater inflows can make a significant difference to the bay salinities, and to the duration, frequency, and severity of high salinity conditions. Id. at 14-15.
Because even small inflows of freshwater can markedly decrease dangerous bay/estuary salinity levels, it would be useful to monitor bay salinities. (Trungale, Day 4, Tr. 15). Then, if salinities reached an agreed upon “warning level,” responsive actions would be triggered, such as reducing water diversions until the salini *747 ties lowered. Id. For example, in Matagorda Bay, a salinity trigger level, known as a “Cumulative Salinity Depletion” (CSD), is incorporated as a condition in one TCEQ issued water permit. Id. Tr. 16; See PX-12 at 7-11 (TCEQ permit granted on April 29, 2011, issued to Lower Colorado River Authority that defines beneficial flow criteria and if the CSD exceeds a certain amount, then certain actions are to be taken).
Defendants and intervenors argue that Mr. Trungale’s models “distort the impact of water diversions in 2008-2009,” because the data may have characterized as “diverted” water than had been impounded years prior. (D.E. 320 at 18). However, Mr. Trungale testified that, given the limitations on available data, his models were “conservative” and, in his opinion, accurate. (Trungale, Day 4, Tr. 48-49) (“it seems very much in the range of what I would expect to see.”). Moreover, no defense witness challenged this aspect of Mr. Trungale’s methodology. Indeed, GBRA witness Dr. George Ward admitted that Mr. Trungale “ran the model correctly.” (Ward, Day 7, Tr. 163). The evidence established that TCEQ’s authorized diversions impact freshwater inflows and in turn, the salinities of the San Antonio bay/Guadalupe estuary.
2. Trungale’s findings anticipated.
Mr. Trungale’s findings were not surprising, and simply confirmed what the Whooping Crane International Recovery Team, USFWS, and TPWD officials had observed and warned about in prior years: decreased freshwater inflows correlate with higher crane mortality. For example, the Whooping Crane International Recovery Plan of 2007, published by the USFWS, recognizes that, in Texas, the largest threat to the AWB flock’s survival is the reduction in freshwater inflows:
Freshwater inflows. Currently, expanding human populations throughout the range of the whooping cranes continue to threaten survival and recovery of the birds. Impacts are particularly severe on the winter grounds. Freshwater inflows starting hundreds of kilometers inland, primarily from the Guadalupe and San Antonio rivers, flow into the Whooping Crane critical habitat at Aransas; these inflows are needed to maintain proper salinity gradients, nutrient loadings, and sediments that produce an ecologically healthy estuary (TPWD 1998). Spring flows originating from the Edwards Aquifer are also crucial, especially in times of drought when they can make up 70% of Guadalupe River water. Inflows are essential to maintain the productivity of coastal waters and produce foods used by the whooping cranes. Coastal waters with low saline levels are maintained by these instream flows, providing drinking water for cranes that would otherwise fly inland for freshwater.
TPWD has recommended target inflow levels needed to maintain the unique biological communities of the Guadalupe Estuary (TPWD 1998), which includes Whooping Crane critical habitat. Unfortunately, mechanisms to guarantee these flows are not provided by Texas water law, and critics have challenged the size of the target inflows.
Upstream reservoir construction and water diversions for agriculture and human use reduce freshwater inflows. Many existing water rights are currently only partially utilized, but greater utilization is expected over time. Water rights continue to be granted on the Guadalupe, and some sections of the river are already over-appropriated.
PX-11 at 21 (emphasis added).
On March 30, 2007, the Executive Director of the Texas Parks and Wildlife *748 Department signed in concurrence with the findings and opinions of the Recovery Plan. (Archibald, Day 1, Tr. 81-82); PX-11. Moreover, the State of Texas has previously recognized the significance of freshwater inflows, with one published study specifically calling for a guaranteed minimum annual inflow of 1.1 million acre-feet for San Antonio bay. (Trungale, Day 3, Tr. 294-295); PX382. A similar recommendation was made in a more recent state study on recommended inflows by TCEQ’s Guadalupe-San Antonio BBEST. (Trungale, Day 3, Tr. 294-295).
In 2009, the USFWS identified the Whooping Crane as one of their “spotlight species,” a species chosen for particular attention and a focus on recovery efforts. See PX-25. The Spotlight Species Action Plan for the Whooping Crane acknowledges that the critical habitat of the AWB flock is threatened, and it specifically addresses water diversions and decreased freshwater inflows:
At Aransas National Wildlife Refuge (NWR) and throughout the central Texas coast, decreases in freshwater inflows from water diversions and reservoir construction add to the following threats: reduction in available main food items at Aransas NWR, the blue crab (Calimetes sapidus) and wolfberry (Lycium carolinianum) [and] Increased intervals when winter marsh salinities exceed the threshold of 23 parts per thousand (ppt) thereby decreasing the availability of fresh drinking water for the cranes.
PX-25 at 1 (emphasis added). As discussed in more detail below, the decreased inflows and higher resulting salinities across the whooping cranes’ habitat causes a reduction in the birds’ primary food resources, blue crabs and wolfberries, as well as drinking water.
3. Dr. Ward’s modeling not reliable.
GBRA witness Dr. George Ward reviewed Mr. Trungale’s modeling. 49 (Ward, Day 7, Tr. 97-98). Dr. Ward was offered without objection as an expert on circulation, salinity, distribution, hydrology and modeling. Id. Tr. 109.
Dr. Ward characterized the San Antonio bay/Guadalupe estuary as a “sluggish responder” to salinity because its exchange with the sea takes place up and down the coast, rather than at a direct entrance. (Ward, Day 7, Tr. 127-28). When a freshwater pulse enters the San Antonio bay/Guadalupe estuary, it displaces water, and if the pulse is large enough, it pushes freshwater into the surrounding estuary and even out into the adjacent Gulf of Mexico. Id. Tr. 128. The salinity then works its way back into the system by tidal exchange, internal circulations, density currents, and turbulence, and these processes are collectively referred to as “salinity intrusion.” Id.
Dr. Ward used the same models as Mr. Trungale (no water diversions, historical diversions, and full permit diversions), and concluded that the average salinity in the San Antonio bay/Guadalupe estuary under the three Trungale scenarios varied only by approximately 1.5 ppt. (Ward, Day 7, Tr. 128). Ward characterized this variance as simply “noise” in the natural variability. Id. Tr. 132-36. Dr. Ward arrived at this conclusion by averaging the geographic distribution of salinities modeled by Mr. Trungale. (Ward, Day 7, Tr. 134) (“Now, to try to compress this variation into something that’s more assimilable to *749 our human minds, I’ve just averaged them.”).
Nowhere does Dr. Ward explain adequately why this manipulated use of average salinity across the entire bay system is a better, or even relevant, measure. To the contrary, Dr. Ward admitted that the key aspect of an estuary is the geographic distribution of salinity gradients:
Q. Now, in your review of — in your critique of Joe Trungale’s work, you didn’t mention anything about geographic coverage, right?
A. That’s correct.
Q. And isn’t, in fact, the geographic distribution of various salinities a key aspect of the estuary?
A. It is.
(Ward, Day 7, Tr. 153); DX-280. And Dr. Ward testified that “the intent of TxBlend is to predict salinity throughout the bayl/estuary].” Id. Tr. 155. Yet Dr. Ward decided that the results of TxBlend are “very complicated” so he chose to “pre-digest” and “summarize” the results in his testimony. Id. His summary consisted of one number — an average salinity — to take the place of thousands of data points describing how salinity changes throughout the bay, both geographically and temporally. DX-424. This manipulation of the data produced no meaningful results for the Court, and did not cast doubt on the conclusion that water diversions result in higher salinities to the San Antonio bay/Guadalupe estuary, the critical winter habitat of the whooping cranes.
4. Dr. Montagna’s observations and studies confirmed Trungale’s modeling.
Dr. Paul Montagna is an expert in Texas estuaries: he is the endowed Chair for Ecosystems Studies and Modeling at the Harte Institute at Texas A & M Corpus Christi; he is a professor of Physical and Environmental Sciences; and he is the Coordinator for the Coastal and Marine Science Doctoral Program. 50 (Montagna, Day 3, Tr. 171). He has worked in primarily two areas: (1) offshore oil and gas and deep sea ecology; and (2) estuarine research related to fresh water inflow. Id. Tr. 173. At the time of trial, he was leading the research for NOAA on the oil spill associated with the Deepwater Horizon blowout. Id. He has studied and attempted to determine the environmental inflows needed for Corpus Christi bay and San Antonio bay. Id. Tr. 174.
Dr. Montagna described an estuary as “a semi-enclosed body of water, where freshwater and marine water mix. (Montagna, Day 3, Tr. 176). Nearly all coastal zones in the world are estuarine environments. Id. There is always movement of water from the tides, and it is the mixing of fresh and marine water that “makes estuaries the most productive environments on earth.” Id.
TAP exhibit PX-59 is a diagram of the habitats and geomorphological components of bar-built estuaries. (Montagna, Day 3, Tr. 178). With Texas coasts, the beach is on a sand bar that essentially separates the bay/estuary from the ocean. Id. Tr. 178. The bay closest to the ocean is referred to as the “primary bay,” and the bay into which the river flows is referred to as the “secondary bay.” Id. There is a gradient in habitats with more marsh habitats and oyster reefs near the rivers, and more beach habitats with sea grass beds near the ocean. Id. Tr. 178-179. The most important aspect of the fresh water inflows is that it creates the very gradient of salinities across the bay to support the variety of communities and organisms that live there. Id. Tr. 181.
*750 Dr. Montagna’s testimony affirmed Mr. Trungale’s modeling that water diversions decrease freshwater inflows to the Refuge. TAP exhibit PX-60 is a diagram of diverted freshwater inflows. (Montagna, Day 3, Tr. 181). When a diversion of freshwater occurs, for example by a dam across a river or impoundment, the water flow is decreased and the dilution power of rain water is lowered, increasing salinity in the bays. Id. Tr. 182. In addition, a reduction in river inflows means a reduction in dissolved nutrients and organic matter to the bay, as well as a reduction in sediments. Id. If sediments get stopped behind a dam, there is less buildup of sedimentation in the marshes, and that could actually cause erosion rates to increase. Id. PX-61 is a conceptual model of inflow effects. Id. Tr. 183. PX-61 demonstrates that freshwater inflows create the estuary conditions in the context of salinity, sediments, dissolved materials, nutrients, organic matter, and also particulate matters. Id. The biology within the estuary responds to the estuary conditions, which are determined by the freshwater inflows. Id. Tr. 183-184.
Dr. Montagna testified about his work on the Science Advisory Committee in connection with another S.B.3 region, the Nueces Bay, which is south of the San Antonio bay/Guadalupe estuary. 51 (Montagna, Day 3, Tr. 187). Although the purpose of the S.B.3 process is to develop environmental flows for the particular bay/estuary system, in the case of the Nueces Bay, it is no longer “ecologically sound.” Id. In the 1930s, the Nueces Bay was low saline and productive. Id. Indeed, the Nueces Bay fossil record reveals that the area once supported large populations of rangia clams, bivalves that required very low salinities, from zero to ten ppt. Id. Tr. at 193. However, as a result of the drought and the two dam systems, including Choke Canyon, conditions in Nueces Bay have changed dramatically; certain areas in Nueces Bay have salinities up to 45 ppt, which is 50 percent greater than sea water. Id. Tr. 188. According to Dr. Montagna, human water management killed the Nueces Bay estuary. Id. Tr. 194.
The Nueces River Basin originates in Edwards County and flows southeast for approximately 315 miles to Nueces Bay near Corpus Christi. The Nueces River basin is located approximately 50 coastal miles to the southwest of San Antonio bay.
Mr. Vaugh is a BBEST scientist for both the San Antonio bay/Guadalupe estuary and for the Nueces Bay/Nueces estuary. In determining the salinity recommendations for the Nueces bay and estuary, the BBEST team chose five indicator species which had known salinity preferences which could be related to freshwater inflow, one of which was the blue crab. (Vaugh, Day 7, Tr. 215-216). The BBEST team recommended a preferred salinity level of 18 ppt for Nueces Bay. Id. However, for the San Antonio bay/Guadalupe estuary, the BBEST team did not use the blue crab. Id. Tr. 213. Dr. Ward acknowledged that, despite the proximately and connectivity of the San Antonio and Nueces bays, the Nueces BBEST researchers employed the boost regression tree and the San Antonio team did not, so the blue crab was not selected *751 as a focal species. Id. Tr. 215. Dr. Ward admitted that this lawsuit was pending at the time of the San Antonio BBEST’s recommendations.
One effort to restore the Nueces Bay is to pipe water directly to the marsh, and the U.S. Army Core of Engineers is conducting a field study concerning a restoration program. (Montagna, Day 3, Tr. 194). However, the system will never support rangia or oysters again. Id. Tr. 195. The Nueces Bay is a cautionary tale for the San Antonio bay/Guadalupe estuary. Id. If water management authorities continue to allow the storing of huge reservoirs of water, the estuarine bays no longer receive significant freshwater inflows, and the Guadalupe estuary could suffer the same high salinities and loss of species life as Nueces Bay/estuary. Id. Tr. 196. However, there is still a chance to save the San Antonio bay/Guadalupe estuary because it is still “in pretty good condition.” Id. Tr. 197. The system can “rebound” from the negative effects of low inflow years if followed by good inflow years. Id. The real challenge is human behavior, because there have always been variations from year to year regarding rain and drought, and the organisms that live there have a certain ability to deal with that variability. Id. Tr. 198. Water diversions are the problem, and in times of drought, “everyone should suffer equally.” Id.
5. Dr. Davis’ modeling.
SARA witness Dr. Stephen Davis is with the Everglades Foundation. 52 In 2003, he helped design the methods for collecting data for a study of the San Antonio Guadalupe Estuarine System (“SAGES”) report. (Davis, Day 8, Tr. 9). The SAGES report was funded by two of the intervenors herein, GBRA and SARA, as well as the San Antonio Water System, an intervenor. (Slack, Day 4, Tr. 143).
For the SAGES report, Dr. Davis examined freshwater inflows and spatial patterns and water quality on three study sites along the north side of the San Antonio bay/Guadalupe estuary. Id. Tr. 13-14. He employed data collected from “TCOON,” the Texas Coastal Ocean Observation Network, which has a series of monitoring sites across the Texas coast, primarily focused in bays and estuaries, that measure everything from water level to wind, salinity, pH, and other water quality parameters. Id. Tr. 14-15. Dr. Davis testified that during “high water” periods, the tidal creeks and ponds on his study sites were connected, but during the “low water” periods, they were separated. Id. Tr. 21-22; DX-400. The terms “high water” and “low water” are not related to high tide or low tide; prolonged periods exist where the pools are either connected or isolated. Id. The longer any pools remain disconnected, the greater the chances are of those pools drying out completely. Id. During a high water period, the estuary is inundated with water that facilitates the connection between bay waters, tidal creeks, and the isolated ponds. Id. Tr. 23. This high water time allows for flushing of the salts that accumulated when water levels are low. Id. During the low water times, the soils become hyper-saline, up to 70 to 100 ppt. Id. The flushing that occurs with high water helps make the soil more favorable for marsh vegetation. Id. For the biota, the high water periods allow access to the estuary for fish, crabs, and other invertebrates. Id. Tr. 24. The estuary is an important source of food, and also provides a refuge against large predators. Id. Tr. 24.
On cross-examination, Dr. Davis admitted that, when prevailing winds come across the coast, water measurements would be higher on the south side of the *752 bay/estuary while dropping on the north side. Dr. Davis’ measurements only included the north side. (Davis, Day 8, Tr. 64). Moreover, his measurements involved areas primarily not located on the Refuge itself. Id. Tr. 65. Dr. Davis did not relate his testimony to Whooping Crane mortality or blue crab abundance. Id. Tr. 60. He did not record any water levels in the bay/estuary during the 2008-2009 winter, nor did he offer any evidence that the tides were particularly low for the 2008-2009 winter.
The testimony of Mr. Trungale, that in 2008-2009, the salinities across the San Antonio bay/Guadalupe estuary would have been lower but for TCEQ’s authorized water diversions, stands un-rebutted.
C. Higher salinities adversely affect blue crabs and wolfberries.
TAP presented evidence that, higher salinities in the bay/estuary, adversely affect the availability of blue crabs and wolfberries, the primary food resources of the cranes. Dr. Montagna testified that presently, the San Antonio bay/Guadalupe estuary typically has a brackish environment, between 15-25 ppt, 53 and the salinity gradient extends across the entire area, which “means that the entire bay winds up being an especially productive habitat.” (Montagna, Day 3, Tr. 200). The system is dynamic and salinity changes can occur day to day, even hour to hour, with tides and other factors. Id. Tr. 201. Also, because it covers a larger area, its productivity is across a wide range of salinities. Id. Tr. 202. Both productivity and resilience to change are a function of habitat size and in these instances, the larger the better. Id.
1. Dr. Montagna on salinity preferences of blue crabs.
In connection with his evaluation of the salinities in different bays, Dr. Montagna has had the opportunity to study blue crabs. (Montagna, Day 3, Tr. 203). TAP’s exhibit PX-68 is a conceptual model of the blue crab life cycle. 54 The cycle begins with an adult female crab and egg sac. Id. The females migrate to the higher salinity zones where they release their eggs into the ocean, but remain close to the pass, where the bay and ocean meet. Id. Tr. 204. The larvae that are released from the eggs pass through a series of stages. Id. Initially, they are plankton and live primarily in the ocean. Id. As the tides come in, plankton have behaviors which allow them to ride the current and move into the bay/estuary when the tide is flooding, and move out of the current when the tide is ebbing, so they do not lose ground, and eventually, the smaller ones wind up in the fresher parts of the bay/estuary further inland. Id. These small crabs seek the estuary because it is rich with nutrients, and this is one reason why estuaries are known as “nurseries” because so many species return to this area for the food supply and to develop and grow larger. Id. Tr. 205. The estuary is the “ideal environment” for young crabs because they can hide from predators in the marshes, and the area is nutrient rich, thus increasing their chances of survival. Id. Tr. 207. Blue crabs are found in basically all salinities, from the ocean to the *753 river mouth, and this gradient of salinities directs the blue crab in its life cycle. Id.
Between 1980 to 2009, there has been a significant decline in blue crab abundance over the entire Texas coast. (Montagna, Day 3, Tr. 208). And see PX-69, graph of blue crab abundance measured in trawls 55 from 1980 to 2009. Over-fishing plays a role in the decline, but while fishing regulations have become more stringent, the blue crab population has still not rebounded. Id. Tr. 209. There is likely a climate component to the decrease. Id. However, there is simply no dispute that “blue crab abundances today are at historic lows, and that the blue crab populations themselves are highly threatened.” Id. Tr. 210. Given the long-term trend, this makes fluctuations in salinities within a particular bay system “critical.” Id.
Another important aspect of salinity is that disease organisms have a preference for higher salinities. (Montagna, Tr. 211). Indeed, when female crabs depart for the ocean to release their egg sacs, the males remain in the lower salinity parts of the bay to avoid parasites. Id.
In 1985, after the TCEQ was first charged with considering the impact to bays and estuaries when a permit is requested, officials looked to see what available data might be useful. (Montagna, Day 3, Tr. 213). The TPWD had previously collected monitoring data which included dissolved oxygen, salinity, temperature, depth of sample, and other information that could be used to examine freshwater inflow needs. 56 Id. Tr. 214. Mr. Trungale employed a statistical model, the Boosted Regression Tree (BRT), 57 to evaluate the existing data from San Antonio bay/Guadalupe estuary. Id. Tr. 213-14, 217. The BRT results confirmed that blue crabs’ preferred salinity range is between 10-20 ppt, with reductions at 22 ppt, and a “sharp drop” above 25 ppt. Id. Tr. 215, 224-25; PX-248.
The BRT regression equation can also be used in combination with the geographical data to predict the distribution of blue crabs and how the distribution changes with salinity. (Montagna, Day 3, Tr. 227-228). Dr. Montagna incorporated the BRT statistical information into a mapping system to graph the relationship between changing salinities and the chance of a Whooping Crane finding a blue crab in that area. Id. Tr. 230-31. See PX-249; PX-250. As expected, with lower salinities, the greater the chances for a Whooping Crane to find a blue crab. Id. Tr. 228.
2. Dr. Miller’s blue crab data.
In rebuttal to Dr. Montagna, defendantintervenor GBRA offered witness Dr. Thomas Miller, the director of the Chesapeake Biological Lab in Maryland. 58 He testified as to the life cycle of the blue crab, and noted that blue crabs need access to high salinities at the zoea 59 stage; however, in direct contrast to Dr. Montagna’s findings, he opined that blue crabs *754 had no physiological need for low salinities. (Miller, Day 7, Tr. 225-35). However, on cross-examination, Dr. Miller agreed that, while the blue crab might not require lower salinities biologically, the estuary and its freshwater inflows provide important nutrients, like nitrogen and phosphorus to the blue crabs. Id. Tr. 257-58. He acknowledged that some plant species necessary to the blue crab’s habitat, such as Spartina altemiflora, require lower salinities. Id. Tr. 259. He admitted that some blue crab parasites are more prevalent in high salinities. Id. Tr. 262. He conceded that, although there are viral infections that exist in freshwater that are more dangerous than parasites, those have only been reported in Mississippi, not Texas. Id. Tr. 265. Thus, Dr. Miller offered no evidence to refute the importance to the blue crabs of the estuarine environment with corresponding freshwater inflows.
Dr. Miller discussed commercial crabbing along the Texas coast as a possible reason for blue crab decline as opposed to freshwater inflows. (Miller, Day 7, Tr. 252). However, he offered no evidence to suggest that commercial crabbing was more extensive in 2008-2009 to have adversely affected the blue crab population, and in turn, the whooping cranes.
In the Recovery Plan, the report cites to a study by Longley in 1994 who determined that: “A simple inverse relation exists between blue crab catch rates and mean salinity within an estuary.” (PX-11 at 21). The Court finds that the preponderance of the accepted and sound scientific evidence establishes that an increase in bay/estuary salinities results in a decrease in blue crab abundance.
3. Wolfberry production.
Dr. Davis testified that salinity is an important factor for wolfberry production. (Davis, Day 8, Tr. 66-70). In his SAGES report, he found that lower salinity levels in the summer led to increased fall fruit production at all three study sites. Id. Tr. 70. He also testified that laboratory experiments confirm lower salinities are better for wolfberry fruit production. Id. GBRA witness Dr. Slack agreed that “having more freshwater inflows is beneficial to wolfberry production.” (Slack, Day 6, Tr. 168,173, 206).
4. Observations and measurements concerning blue crab abundance and wolfberry availability in 2008-2009.
As will be discussed in more detail below, the crane experts each testified as to the importance of the blue crab and wolf-berry fruit in the crane diet, and their personal observations were confirmed by fecal studies. (Archibald, Day 1, Tr. 73; Chavez-Ramirez, Day 2, 73-77). Mr. Stehn testified that, in 2008-2009, wolfberry production in the fall was “notably less than average.” (Stehn, Day 3, Tr. 28-29). Both Mr. Stehn and Dr. Chavez-Ramirez noted significantly reduced blue crab catchings by the cranes that winter. See PX-22. The preponderance of the credible evidence establishes that decreases in freshwater inflows to the San Antonio bay/Guadalupe estuary results in a decrease in blue crabs as well as wolfberries on the critical habitat of the AWB cranes.
D. Statistical modeling confirms higher salinities are associated with higher crane mortality on the Refuge.
TAP witness Dr. Ronald Sass is the former chair of Ecology and Evolutionary Biology at Rice University, and is currently an Emeritus Professor, a fellow of the Baker Institute of Public Policy, author of 165 peer-reviewed papers, including one on whooping cranes, and a shared recipient of the 2007 Nobel Peace Prize as a member of the Intergovernmental Panel on Climate *755 Change. (Sass, Day 1, Tr. 177-180). He is a biogeochemical expert in earth systems, including hydrologic and ecological aspects, and the statistical analysis of those systems. 60 He was asked to investigate the relationship between freshwater inflow and AWB crane mortality. (Sass, Day 1, Tr. 182-83). Using Mr. Stehris mortality data, and freshwater inflow data, PX-266, Dr. Sass found a statistically significant association between years of high crane mortality and low July through December freshwater inflows. (See e.g. PX-75, a graphic representation of the relationship between AWB crane mortality with freshwater inflow into the San Antonio bay estuary system; PX-76, Bar graph of Whooping Crane mortality and freshwater inflows).
Dr. Sass employed the Fisher Exact Probability Test to test the hypothesis that high crane mortality is associated with low freshwater inflows. (Sass, Day 1, Tr. 198, 206); PX-265. He concluded that low inflows and high mortality are “causally correlated” and “in all cases of high mortality you have low river flow, no exceptions really.” Id. Tr. 209-210. This conclusion is scientifically supported and explained by the biological reasons in the extensive literature. Id. Tr. 183-185.
TAP witness Dr. Kathy Ensor is the current chair of the Statistics Department at Rice University and a fellow of the American Society of Statistics, among many other honors. 61 She is highly recognized as an environmental statistician. Dr. Ensor reviewed Dr. Sass’s statistical results, and confirmed that he applied the Fisher Test correctly and appropriately. (Sass, Day 1, Tr. 238). The result of the Fisher Test, (p-value = 0.02), demonstrates that there is a strong association between the level of freshwater inflows into San Antonio bay/Guadalupe estuary and AWB crane mortality. (Ensor, Day 1, Tr. 239). Additional statistical tests using the same data as Dr. Sass confirmed the statistically significant correlation. Id. Tr. 240. A significant relationship between levels of freshwater inflow to crane mortality means not occurring by chance. A Poisson Count Regression found a strong relationship (p-value < 0.0001) between low inflows and high mortality. (Sass, Day 1, Tr. 241); PX-27; PX-28. Statistics can support a finding of causation when paired with a scientific argument or a biological explanation for that causation and here it does so support. (Ensor, Day 1, Tr. 241-242).
As rebuttal to Drs. Sass and Ensor, GBRA offered Samuel Vaugh, a registered professional engineer who is employed at HDR Engineering in Austin. 62 His expertise is in river basin hydrology, regional water supply planning, water rights permitting, river basin modeling, and statistical analyses. (Vaugh, Day 7, Tr. 173-74). He serves on three BBESTs including the San Antonio bay/Guadalupe estuary, as well as for Nueces, and Sabine-Neches. Id. Tr. 177. He served as a member on the Edwards Aquifer Habitat Conservation Plan. Id.
Mr. Vaugh testified that his current employer, HDR Engineering, provides services to two intervenors, GBRA and SARA. (Vaugh, Day 7, Tr. 202). He reran Dr. Sass’ analysis concerning freshwater inflows and crane mortality, and he “did get the same answer.” Id. Tr. 207. He also ran a number of statistical tests, but he did not use winter crane mortality, but instead, annual crane mortality. Id. Tr. 208-209. He decided that winter crane mortality was not a reliable count and instead viewed the health of the ABW *756 crane “as a year round process.” Id. Tr. 209. However, he admitted that he had no scientific basis for employing annual mortality: he is not an ornithologist or a naturalist or a biologist. Id. Tr. 210. The Court ruled that Mr. Vaugh was not qualified as an expert on selecting crane mortality data and applying it statistically. Id. Tr. 212.
E. At least 23 Whooping Cranes died on the Refuge in 2008/2009.
In 1941, the total population of Whooping Cranes worldwide had been reduced to just 15 birds. 63 (Archibald, Day 1, Tr. 59). Through conservation efforts, the AWB flock has slowly grown to that of almost 300 birds. 64 Id. As such, the AWB flock has become an international symbol of conservation success, “recovering from the brink of extinction.” 65 Id.
Testimony regarding the many deaths of AWB cranes in 2008-2009 came primarily from three witnesses: Dr. George Archibald; Dr. Felipe Chavez-Ramirez, and Mr. Tom Stehn. Dr. Archibald, Dr. Chavez-Ramirez, and Mr. Stehn, have been recog *757 nized as the leading authorities in their fields of biology, ornithology, and whooping cranes in particular. Dr. Archibald is a renowned expert on all cranes of the world, and he has been actively involved in Whooping Crane conservation efforts since 1966. 66 (Archibald, Day 1, Tr. 56). Since 1990, he has been a member of the International Whooping Crane Recovery Team, a joint effort between Canada and the United States to identify the problems facing Whooping Crane sustainability and to propose solutions to those problems. 67 Id. Tr. 57-58. He is co-founder of the International Crane Foundation, and a MacArthur Fellow. Id. Tr. 59.
Dr. Felipe Chavez-Ramirez is currently employed by the Gulf Coast Bird Observatory in Lake Jackson, Texas, a nonprofit conservation organization created to protect the migratory bird habitat along the Gulf Coast of Mexico. 68 (Chavez-Ramirez, Day 1, Tr. 253). He is a member of the International Whooping Crane Recovery Team and of the International Union for Conservation of Nature (IUCN) Crane Specialist group. Id. He conducted his PhD research on foraging and energetics of cranes at the Aransas Refuge during the winters of 1992-1993 and 1993-1994, 69 and he continued with over two decades of field research on the AWB flock. Id. Tr. 253-303.
Mr. Tom Stehn was the Refuge’s biologist for 29 years, and he developed a methodology for counting the AWB cranes via aerial surveys and crane behavior. 70 (Stehn, Day 2, Tr. 296-297). He served as the USFWS’ International Whooping Crane Coordinator and as a Recovery Team leader. Id. Tr. 297. As the Refuge biologist, he authored the USFWS’ annual report on the status of the AWB flock from 1985 until his retirement in 2011, including a special report concerning the 2008-2009 winter. 71 Id. Tr. 298. He has published 16 additional Whooping Crane manuscripts that were subject to peer-review. Id. Tr. 298.
1. Counting cranes is rooted in crane behavior.
Dr. Archibald, Dr. Chavez-Ramirez and Mr. Stehn each testified and recognized that the task of counting cranes, and implicit thereto, determining a crane’s ab *758 sence or demise, is rooted in an understanding of the cranes’ basic biology and behavior. Due to their size and color, cranes are highly detectable and conspicuous on their wintering grounds. 72 (Archibald, Day 1, Tr. 78). (See also PX-263, photograph of three whooping cranes; and DX-61, which includes hundreds of photographs of the AWB cranes). Crane families are cohesive and stay physically close together. (Archibald, Day 1, Tr. 73; Chavez-Ramirez, Day 1, Tr. 282-287). A juvenile will remain between 20 to 50 meters of one parent, and will immediately run to the parent if there is a disturbance or noise. (Chavez-Ramirez, Id.)
The AWB flock typically arrives at the Aransas Refuge in late October each year, with each family unit returning to its specific territory from years’ prior. (Archibald, Day 1, Tr. 72-73). The territories are between 200 to 400 acres. Id. Whooping cranes are territorial and will aggressively defend their defined territory against other individuals of the same species. (Chavez-Ramirez, Day 2, Tr. 82). By excluding other members of the same species, the crane is maintaining access to all the resources within the boundaries of the territory for itself, mate, or offspring. Id. Tr. 83. Whooping cranes are territorial on their breeding grounds in Canada, and also on their wintering grounds at the Refuge. Id. The only purpose for defending a territory at the wintering grounds is to procure food resources, because there is no nest to protect and the bird already has a mate. Id. Tr. 84. (And Archibald, Day 1, Tr. 73, winter territories protect resources).
As migratory birds, the AWB flock demonstrates site fidelity. (Chavez-Ramirez, Day 2, Tr. 84). This means that the same individual birds return to the same exact location on the Refuge year after year. Id. This behavior has been confirmed by banding, as the same banded cranes return to their same established territories each winter. Id. Tr. 85. In addition to site fidelity, whooping cranes exhibit site tenacity, which is the behavior of the whooping cranes to maintain their established territories. Id. Tr. 87. Site tenacity has been demonstrated via the aerial surveys which show the same birds returning to, and remaining on, their specific site each winter. Id.
2. Tom Stehn determined peak population numbers for the USFWS.
As part of the international recovery effort, the USFWS has regularly monitored the whooping cranes at the Refuge, which is more accessible than the remote Canadian province where the birds summer. (Chavez-Ramirez, Day 1, Tr. 73). Part of that monitoring includes population counts which have been conducted through aerial flights dating back to the 1950s. 73 (Stehn, Day 2, Tr. 290). Stehn has conducted these flights for 29 years, longer than any other USFWS employee.
Stehn’s first aerial census flight was in the fall of 1982. (Stehn, Day 2, Tr. 289). Census flights had been conducted prior to that time, dating back to 1950, and performed on a weekly basis. Id. Tr. 90. Stehn flew with an experienced pilot, Robert Tanner, who had flown for the previous *759 refuge biologist, in a Cessna 152. Id. Stehn observed how things had been done in the past, and then, from year to year, the program evolved and he had significant input into the census methodology. Id.
Both aluminum and color banding of whooping cranes began in 1981, so when Stehn first conducted aerial counts, he was able to utilize banding to help identify individual cranes. (Stehn, Day 2, Tr. 290-291). To conduct a survey, the pilot would drop the plane from approximately 200 feet to between 20 to 50 feet above the marsh and salt flats of the estuary, and fly just to the side of the cranes. Id. Tr. 291— 292. Using his naked eye, not binoculars, Stehn would record the color bands he observed. Id. Tr. 292. Any crane could have as many as four bands, and multiple passes were made to record all of the information. Id. In more recent years, Stehn did not employ as many low passes because the color banding had faded. Id. Tr. 293. In addition, they were now flying a different plane, a Cessna 210, making slower speeds less safe. Id. Finally, federal regulations limited flight time while, simultaneously, the range of crane territories increased, and so in 2007-2008, low pass counting was eliminated. Id. Thereafter, aerial surveys in the Cessna 210 were conducted at approximately 200 feet for the duration of the flight. Id. Tr. 294.
Each fall, in preparation of the cranes’ arrival, Stehn began assessing the habitat, performing crab counts in October, while also monitoring salinities. (Stehn, Day 2, Tr. 302). He would receive calls from the public along the migration route of the cranes notifying him about a possible sighting. 74 Id. Stehn would verify the sighting and effectively monitor the flock as it made its way south to the Aransas Refuge. Id. Tr. 302-303. Once the birds arrived, he would begin his aerial surveys. Id. 304. From 1982 through September 2011, he was on all but two flights. Id.
Mr. Stehn’s preference was to conduct a census flight every week, with a total of 26 flights per season. 75 (Stehn, Day 2, Tr. 304). In recent years, due to increased expenses and funding cutbacks, the number of flights was reduced to between eight to twelve a season. Id. The aerial flights enabled Stehn to verify the location and mapping of territories (on the early flights); identify the mated pairs with their juveniles; determine peak population; record evidence of mortality; record evidence of mate switches; verify habitat use of AWB crane families; observe crane movement outside of the typical winter grounds; and record sightings of banded cranes. Id. Tr. 308. On the aerial counts, Stehn was: “... finding every bird, to the best of my ability. And we are covering every location where I believe a Whooping Crane may be.” Id. Stehn also used watercraft to search for cranes.
In general, a flight would take 7.5 hours. 76 (Stehn, Day 2, Tr. 309). When *760 visibility was good, file-mile sections divided into quarter-mile grids were flown. Id. Tr. 310. When visibility was an issue, the quarter-mile grids were reduced to 200 meters. Id. Tr. 310. During the flights, if there was a deviation from the transect route, grids would be repeated to ensure that the total known range of the AWB flock had been covered. Id. Tr. 311. If birds were missing from their known territory, the territory would be revisited and the birds searched for at surrounding watering holes or uplands. Id. Tr. 311-312. Each sighted crane was marked on a map of the territories, along with a checklist of known crane families, to build towards the peak population number as well as to determine if a crane disappeared from its previously observed territory. Id. Tr. 313-314. During the return leg of the five-mile transect, previously observed cranes were confirmed. Id. Thus, for most flights, Stehn was able to see each territory at least twice each flight. Id. Immediately after the flight, Stehn reviewed the results of his counts while it was “fresh in [my] mind.” Id. Tr. 315. Stehn has been observing some of the same cranes since 1982 and can identify individuals. Id. Tr. 317. Stehn’s recognition of each individual crane enabled him to build “from week to week on what is out there” and ensure the accuracy of the counts. Id.
With the information gathered on these winter flights, Stehn determined a peak flock number each winter. To get the peak population number for the winter, Stehn analyzed the counts from the various flights. He calculated that, on an average flight, he was seeing approximately 95% of the flock. (Stehn, Day 2, Tr. 319). Dr. Chavez-Ramirez confirmed this estimate. (Chavez-Ramirez, Day 2, Tr. 56-57) (stating the percentage of cranes counted was between upper nineties and mid eighties depending on the flight). The peak population number for 2008-2009 was 270. (Stehn, Day 2, Tr. 320); PX-22 at 21.
GBRA witness Dr. Michael Conroy did not challenge the peak populations counts of Mr. Stehn, as adopted and published by the USFWS.' In fact, Dr. Conroy expressly agreed that Stehn’s peak flock size counts were “reasonably accurate.” (Conroy, Day 8, Tr. 90).
3. Crane mortality counts.
In addition to the peak flock number, Stehn determined winter crane mortality. His methodology for counting crane mortalities was basically the same as for determining population counts because both counts happened on the same aerial survey. (Stehn, Day 2, Tr. 308). Like population counts, Stehn’s methodology for counting AWB crane mortality was based on crane biology and “behavior, of what I have been observing for 30 years.” Id. Tr. 321.. To determine mortality, Stehn did not simply subtract one population count from another. Id. Instead, Stehn counted a mortality if a bird went missing from its known territory on two or more flights and was not relocated on subsequent flights. Id. Tr. 324. That is, Stehn’s mortality calculation was based on the sustained absence of a crane from its territory. 77 Id. Tr. 321-322. If a crane disappeared from its known territory and did not return for the remainder of the winter, Stehn could reasonable conclude that the bird had died. Id. Tr. 324. Stehn did not declare a mortality of an adult bird without repeated confirmation. Id. Tr. 327; Day 3, Tr. 61-62.
Stehn employed the same method to count juvenile mortalities because “the chick is always with the parents.” 78 *761 (Stehn, Day 2, Tr. 327). On the rare occasions when a juvenil

[Text truncated at 120,000 characters. The full text is on the page linked above.]

---

Source: Frix Law Library, https://www.frixlaw.com/law-library/cases/8706784. Public record. Not legal advice.