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Rivers v. United States Army Corps. of Engineers

July 12, 2003


The opinion of the court was delivered by: Gladys Kessler, United States District Judge.


Plaintiffs, a number of national and local environmental organizations,*fn1 brought suit against the United States Army Corps of Engineers ("Corps"), the Secretary of the Army, the United States Fish and Wildlife Service ("FWS"), and the Secretary of the Interior (collectively,"Defendants" or "Federal Defendants"), *fn2

seeking to protect the endangered least tern, the endangered pallid sturgeon, and the threatened Great Plains piping plover, all of which are protected by the Endangered Species Act ("ESA"), 16 U.S.C. §§ 1531, et seq. Plaintiffs allege that the manner in which the Corps has operated the extensive dam and reservoir system on the Missouri River and the manner in which the FWS has carried out its statutory responsibilities under the ESA have adversely impacted the three species in question. Plaintiffs assert claims against the Corps and the Secretary of the Army under the ESA, the Flood Control Act of 1944 ("FCA"), 33 U.S.C. §§ 701, et seq, and the Administrative Procedure Act ("APA"), 5 U.S.C. §§ 701, et seq, and assert ESA and APA claims against FWS and the Secretary of the Interior.

This matter is now before the Court on Plaintiffs' Motion for Preliminary Injunction and Defendants' Motions to Strike.*fn3 A motions hearing in this matter was held on July 2, 2003. Upon consideration of the Motions, Oppositions, Replies, amicus curiae and intervenor briefs, the arguments presented at the motions hearing, and the entire record herein, for the reasons discussed below, Plaintiffs' Motion for Preliminary Injunction is granted, and Defendants' Motions to Strike are denied as moot.


This is an immensely difficult case with great ramifications for the Missouri River Basin. Because of its complexity, it is important to clarify and summarize the factual and legal issues presented.

The Missouri River Basin--one of the largest and most bountiful in our country--is home to hundreds of species of birds, fish and insects, as well as the habitat which supports their existence. Three of those species--the least tern, the Great Plains piping plover, and the pallid sturgeon--are in great danger of extinction.

In 2000 the Fish and Wildlife Service issued, pursuant to the Endangered Species Act, a comprehensive Biological Opinion outlining what measures must be taken by the Corps of Engineers in its management of the Missouri River to insure the survival of those three species. These measures are necessary to both protect the three species from further harm and to affirmatively take action to insure their recovery. The Biological Opinion considered time to be of the essence in implementing them. The 2000 Biological Opinion was peer reviewed by government scientists and by an arm of the National Academy of Sciences. It is undisputed that all parties consider it to be the controlling biological opinion.

A central premise on which the 2000 Biological Opinion rests is the need to change the Corps' management of the Missouri River. In particular, the 2000 Biological Opinion calls upon the Corps to institute a water management regimen in which water flows will rise in the spring at least once every three years and decrease every summer. Adoption of this operating principle would: encourage breeding of the least tern and piping plover in the spring; avoid flooding of their nests and habitat, as well as killing of their chicks, in the summer; increase the numbers of prey-fish available for juvenile pallid sturgeon to feed on; and provide a more receptive environment in which juvenile pallid sturgeon would thrive.

In October of 2002, the Corps released a draft Annual Operating Plan for the River presenting two potential flow regimes. Neither plan implemented the spring rise or summer flow regime that the 2000 Biological Opinion found necessary to protect the three species from extinction. When the Corps released its final Annual Operating Plan in January 2003, it contained no provision for a spring rise and low summer flow regime for managing the River. Plaintiffs in this case then filed suit, seeking to force the Corps and FWS to comply with federal law and protect these three endangered and threatened species.

In 2003, the Fish and Wildlife Service did a total about-face, issuing a new Biological Opinion that reversed the position it took in 2000. Looking only at Corps activities in the summer of 2003, FWS concluded that the three species could survive one more summer without the summer low flow that was previously deemed essential to both avoid current harm and advance future recovery. Moreover, FWS stated that its change of position rested on the assumption that the Corps' future management of river flows would be consistent with the recommendations made in the 2000 Biological Opinion.

There is no question that the three species (the least tern, the piping plover, and the pallid sturgeon) will suffer irreparable harm if the Corps is allowed to carry out its 2003 Annual Operating Plan. Two of those species--the least tern and the pallid sturgeon--have been declared"endangered" under the Endangered Species Act and are on the verge of extinction; the piping plover has been declared"threatened," which means that without protection, it will also face extinction. There is no dollar value that can be placed on the extinction of an animal species--the loss is to our planet, our children, and future generations.

Upon analysis of the lengthy legal arguments presented by all parties, the Court finds that there is a substantial likelihood that Plaintiffs will prevail on the merits of their case for the following reasons: FWS has failed to adequately explain or justify its reversal of position from its 2000 Biological Opinion to its 2003 Biological Opinion; FWS' 2003 Supplemental Biological Opinion is premised on a totally baseless assumption--namely that the Corps will adopt a River management plan for 2004 that will be consistent with the 2000 Biological Opinion; and FWS' 2003 Supplemental Biological Opinion improperly segments its analysis and narrowly focuses on harms to the species only during this summer instead of considering all present and future effects on the three imperiled species. Finally, because the 2003 Supplemental Biological Opinion is arbitrary and capricious, it cannot serve to validate the Corps' management plan that will lead to harm of these three species in violation of the Endangered Species Act.

In addition to the irreparable harm to the three protected species and the likelihood that Plaintiffs will ultimately succeed in their case against the Corps and FWS, the Court must also consider and balance the various impacts of granting an injunction. There is no question that other interests will suffer if the preliminary injunction that Plaintiffs request is granted. Commercial and consumer interests in the lower Basin states, such as Nebraska and Missouri, will be affected. Navigation will be interrupted for the remainder of the summer and barge companies will lose revenues. Water quality may be affected and there may well be higher water purification costs. Hydroelectric resources will be affected, and consumers may suffer higher costs. However, despite a similar--but shorter--interruption of high water flows last summer caused by drought, none of the Defendants or Intervenors could provide the Court with reliable figures on the extent or certainty of losses. Significantly, when the Corps previously examined the effects of implementing a management plan with summer low flow, it concluded that it would produce an overall net economic benefit to the entire Missouri River Basin.

Balancing the irreplaceable and unquantifiable loss of three species against the concrete--albeit uncertain--impacts on consumers, businesses, and the economies of several States is a daunting task. However, the loss of species is just that irreplaceable. The American people, through their representatives in Congress, have spoken in the"plainest of words" making it abundantly clear that the protection and preservation of endangered species is one of the nation's highest priorities. Tennessee Valley Authority v. Hill, 437 U.S. 153, 194 (1978). For these reasons, as more thoroughly explained in this Memorandum Opinion, the Court concludes that the Plaintiffs' request for a preliminary injunction should be granted.


The Missouri River flows 2,340 miles from its head waters near Three Forks, Montana, to its confluence with the Mississippi River at St. Louis, Missouri. The Missouri River Basin covers the states of Colorado, Iowa, Kansas, Minnesota, Missouri, Montana, Nebraska, North Dakota, South Dakota, and Wyoming, as well as a small part of Canada. Approximately ten million people, including 28 Native American Tribes, live in the Basin.

A. The Flood Control Act

Pursuant to the FCA, Pub.L. No. 78-534, 58 Stat. 887 (1944), and several other federal statutes, Congress entrusted the Corps with managing the Missouri River Basin through its construction and operation of the Missouri River Main Stem System of Dams and Reservoirs ("Main Stem System"). 58 Stat. 591. In completing the Main Stem System, the Corps constructed six dams and reservoirs on the upper part of the Missouri River and narrowed and deepened the lower part of the river for commercial barging.*fn4 Under the FCA, the Corps is responsible, not only for constructing and managing various dams and their corresponding reservoirs, 16 U.S.C. § 460d, but also for contracting for use of surplus reservoir water and promulgating regulations for the use of water stored in the reservoirs, 33 U.S.C. § 708, 709. The FCA also identified various substantive interests that the Corps was to consider in managing the Missouri River Basin, such as flood control and navigation, as well as irrigation, recreation, fish, and wildlife. See 58 Stat. at 889-91. Thus, in enacting the FCA, Congress "provided the Corps with a wide array of interests to consider in regulating the River." South Dakota v. Ubbelohde, 330 F.3d 1014, 1020 (8th Cir. 2003).

1. The Master Manual and Annual Operating Plans

In order to fully consider the wide array of interests the FCA requires the Corps to balance in its management of the Missouri River, the Corps adopted a specific management plan, called the Missouri River Main Stem Reservoir System Reservoir Regulation Manual, or Master Manual, in 1960. Section 9 of the Master Manual sets out a general approach for reservoir operation projects, with a sequential consideration of the various interests identified in the FCA itself. Thus, the Master Manual directs the Corps to consider, in order of priority, flood control, irrigation, water supply and water-quality requirements, navigation and power, and finally recreation, fish, and wildlife. See Fed. Defs.' Ex. 2 ("Master Manual") at IX-1,2.

In addition to this general approach, the Master Manual includes specific technical guidelines for minimum water flows that are to be maintained along the River and methods for calculating the length of the navigation season based upon that minimum water flow at certain times of the year. Master Manual Section at IX-6-9. The Master Manual also directs the Corps to develop Annual Operating Plans ("AOPs"), describing the Corps' management plan for operating the Missouri River water flow in each water year. Master Manual at IX -20, pts. 9-47, 48.

Since its original promulgation in 1960, the Corps has revised the Master Manual three times--in 1973, 1975, and 1979. The Corps has been in the process of producing the latest revision of the Master Manual since the late 1980's. However, after more than ten years of work and multiple assurances to various courts that the latest revision would soon be completed, see South Dakota v. Bornhoft, No. CV 91 26 JDS-BLG, slip op. (D. Mont. Feb. 3, 1993), Ex. 7 to Pls.' Schneider Decl. and Ubbelohde, 330 F.3d at 1020, the Corps has not yet completed its revision of the Master Manual. The present management of the River is still based on the general approach articulated in the 1979 version of the Master Manual.

2. Prior FCA Litigation Involving the 2002 AOP

In response to severe drought conditions that the Missouri River Basin has been experiencing for the past few years, a series of cases were filed in the courts of the Eighth Circuit during the 2002 water year, challenging the Corps' operation of the Main Stem System under the APA and the FCA.*fn5 The unavoidable management constraints caused by the drought led to sharp conflicts amongst the Upper Basin and Lower Basin states as to the priority to be given in the Corps' formulation of the 2002 AOP for allocating the limited supply of water from the Missouri River.

The Corps' 2002 AOP provided that water from a reservoir in South Dakota would be released to maintain downstream navigation on the Missouri River while water levels at the other five reservoirs would be held constant. In order to protect recreational fishing interests, the State of South Dakota filed suit in the federal District Court in South Dakota, and the District Court entered a temporary restraining order, and then a preliminary injunction, requiring the Corps to maintain the water level at South Dakota reservoirs until the end of the spawning season. See, generally, Ubbelohde, 330 F.3d at 1021 (describing the events in South Dakota v. Ubbelohde, Civ. No. 02-3011 (D.S.D.)).

The Corps then announced plans to lower water levels in a North Dakota reservoir in order to achieve the same goal and, predictably, the State of North Dakota brought suit in the federal District Court in North Dakota to enjoin the Corps from lowering the reservoir. The District Court in North Dakota then entered a temporary restraining order, which was later converted into a preliminary injunction, requiring the Corps to maintain that reservoir's water level. See, generally, Ubbelohde, 330 F.3d at 1021-22 (describing the events in State of North Dakota v. Ubbelohde, Civ. No. A1-02-059 (D.N.D.)).

In response to these injunctions that would have harmed downstream navigation interests, the State of Nebraska went to the federal District Court in Nebraska seeking to require the Corps to manage the Missouri River according to the Master Manual and the 2002 AOP. The District Court in Nebraska subsequently entered an injunction ordering the Corps to abide by the Master Manual and 2002 AOP to provide for downstream navigation. See, generally, Ubbelohde, 330 F.3d at 1022 (describing the events in Nebraska v. Ubbelohde, Case No. 8-02CV217 (D. Neb.)).

The Corps immediately appealed each of these injunctions and the Eighth Circuit stayed them on May 22, 2002, noting that "the injunctions in North Dakota and South Dakota expired by their own terms on May 25, 2002," although the injunction in Nebraska did not expire. Ubbelohde, 330 F.3d at 1022. On June 4, 2003, the Eighth Circuit struck down the North Dakota and South Dakota injunctions while upholding the Nebraska injunction. The court found that the North Dakota and South Dakota injunctions were not based on a likelihood of success on the merits. The court held that the 2003 AOP was not arbitrary and capricious because the Corps had "provided a rational basis for its decision to lower one reservoir per year during drought conditions." Id., at 1032. The court also found that the Nebraska District Court's injunction was appropriate because the Master Manual was binding upon the Corps, and therefore the Corps could be ordered to "abide by its own formally adopted policies" in the Master Manual requiring it to manage the River to maintain downstream navigation. Id., 330 F.3d at 1033. The Endangered Species Act was never mentioned in the Eighth Circuit opinion.

B. The Endangered Species Act

In 1973, Congress enacted the ESA "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 and threatened species." 16 U.S.C. § 1531(b). At that time, the ESA"represented the most comprehensive legislation for the preservation of endangered species ever enacted by any nation." Tennessee Valley Authority v. Hill, 437 U.S. 153, 180 (1978)("TVA").

Under Section 4 of the ESA, the appropriate government agency, in this case FWS, conducts a review of the species' biological status and threats to its existence, and then lists the species as either threatened or endangered based on the "best scientific and commercial data available." 16 U.S.C. § 1533(b)(1)(A). Section 4 also requires the listing agency to designate "critical habitat" for endangered and threatened species, i.e., those areas with physical and/or biological features essential for conservation of the species. 16 U.S.C. § 1533(b)(2). Subsequently, listed species and critical habitat are afforded considerable protections, and all federal agencies must assume special responsibilities to conserve them.

Under Section 7 of the ESA, every federal agency must"insure" that"any action authorized, funded, or carried out by such not likely to jeopardize the continued existence of the endangered species or threatened species or result in the destruction or adverse modification of habitat of such species." 16 U.S.C. § 1536(a)(2). In order to avoid jeopardy to endangered and threatened species, federal agencies are required to verify that their actions will not jeopardize any listed species by consulting with and obtaining the assistance of specific federal consultation agencies, such as the Secretary of Interior acting through the FWS. 16 U.S.C. § 1536(4). Federal agencies must use"the best scientific and commercial data available," 16 U.S.C. § 1536(a)(2), to determine if any listed species is present in the area affected by a proposed project and must confer with the Secretary whenever an action is likely to affect such a species. 16 U.S.C. § 1536(a)(3).

As a result of Section 7's consultation requirement, FWS formulates a Biological Opinion ("BiOp")--a comprehensive examination of"whether the action is likely to jeopardize the continued existence of a listed species or result in the destruction or adverse modification of critical habitat." 16 U.S.C. § 1536(b)(3)(A); 50 C.F.R. § 402.02. If the BiOp concludes that the proposed agency action will jeopardize a listed species, the BiOp must include the reasonable and prudent alternatives ("RPAs"), "if any," to the agency's action plans. Id.

Under Section 9 of the ESA, it is unlawful for any person to "take" a listed species. 16 U.S.C. § 1538(a)(1)(B). Accordingly, if FWS determines that the action agency's implementation of RPAs could still result in"an incidental taking" of the listed species, FWS must issue an Incidental Take Statement. That Statement authorizes a specified level of "incidental take" of listed species that "result from, but are not the purpose of, carrying out an otherwise lawful activity conducted by the Federal agency." 50 C.F.R. § 402.02; see also 16 U.S.C. § 1536(b)(4). An incidental take statement must specifically state the impact that agency take will have on the species, identify the "reasonable and prudent measures" ("RPMs") considered necessary to minimize the expected impact, and establish "terms and conditions" necessary for implementation of the RPMs. 16 U.S.C. § 1536(b)(4); see also 50 C.F.R. § 402.14(i). Under the ESA, a take that complies with an Incidental Take Statement is exempt from the ESA's prohibitions and penalties against taking a listed species, 16 U.S.C. § 1536(o)(2). If the agency fails either to implement the RPMs or to comply with the terms and conditions of the statement, any take is unlawful. 50 C.F.R. § 402.14(i)(5).

1. Listing of Species in the Missouri River Basin

Since the enactment of the ESA, a number of species that reside in the Missouri River Basin have been listed as threatened or endangered due to the Corps' physical alteration of the Missouri River and its manipulation of the River's water flow.

In 1985, FWS listed the least tern (Sterna antillarum), a small, fish-eating bird that historically nested on exposed sandbars on the Mississippi and Missouri Rivers. In listing the tern as endangered, FWS found that the Corps' alteration of Missouri River flow patterns had destroyed the sandbars necessary for the species to nest and raise its chicks. 2000 BiOp at 84.

The Great Plains piping plover (Charadrius melodus) is a migratory bird, which grows to approximately seven inches in length and, like the least tern, uses exposed sandbars for its nesting and forage sites. In 1986, FWS listed the Great Plains piping plover as threatened, finding that the Corps'"[d]amming and channelization of rivers [had] eliminated nesting sandbar habitat along hundreds of miles of rivers in the Dakotas, Iowa, and Nebraska." 50 Fed. Reg. 50,731. Subsequently, in September 2002, FWS designated approximately 767 miles of the Missouri River as critical habitat for the piping plover, finding that the features and habitat characteristics of those portions of the Missouri River were essential to plover survival. 67 Fed. Reg. 57,638, 57,642.

The pallid sturgeon (Scaphirhynchus albus) is a large fish that exists primarily in the Missouri River, can live more than fifty years, and can grow to more than six feet in length and 80 pounds in weight. Pallid sturgeon naturally spawn in the spring, cued by rising water levels and water temperatures, 2000 BiOp at 103, and juvenile sturgeon spend the summer and fall in shallow, slow flowing water foraging on populations of small fish found in those waters. 2000 BiOp at 112-113. In 1990, FWS listed the pallid sturgeon as endangered, finding that "[a]lteration of habitat through river channelization, impoundment, and altered flow regime has been a major factor in the decline of this species." 55 Fed. Reg. 36,645.

2. History of the Corps' ESA Consultation for the Missouri River Basin

a. The 1990 BiOp

In 1989, the Corps initiated formal consultation with FWS under Section 7 of the ESA, after FWS listed the tern and plover under the ESA. In November 1990, FWS issued a biological opinion (the "1990 BiOp") and concluded that the Corps' dam operations on the Missouri River were jeopardizing the survival of the two listed birds by directly "taking" these species through flooding of their nests and damaging their habitats in other enumerated ways. 2000 BiOp at 5, 206.

Beginning in 1991, FWS advised the Corps that it needed to supplement the 1989 consultation for the following reasons: the listing of the pallid sturgeon as an endangered species, the Corps' lack of compliance with the bird RPAs in the 1990 BiOp, and

"significant changes to [the Corps'] annual operations since 1990 [BiOp]." 2000 BiOp at 1. The Corps initiated informal consultations relating to its specific actions managing the Missouri River but held off initiating a formal consultation until "sufficient data on project effects and pallid sturgeon life history and habitat use were available as part of the Master Manual Review and Study." Id.

In 1993, the Corps initiated formal ESA Section 7 consultation with FWS regarding revision of the Master Manual, and in April 1994, FWS produced a draft BiOp to be used in the Master Manual revision process. 2000 BiOp at 7, 9. However, after numerous extensions of the Master Manual consultation, the Corps never provided any comments on the 1994 draft BiOp. Id. at 10. In 1997, FWS requested that the Corps reinitiate consultation under the present Master Manual (which was still the 1979 version), given that the "(1) reasonable and prudent alternatives of the 1990 consultation and Biological Opinion for meeting interior least tern and piping plover fledge ratios and habitat have not been met, (2) reasonable and prudent measures to minimize take have not been met, (3) the terms and conditions that implement the reasonable and prudent measures have not been met, and (4) the Corps has not complied with the annual reporting requirements of the ...

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