Rio Grande Silvery Minnow v. Bureau of Reclamation, called Rio Grande Silvery Minnow v. Keys[a] in its earlier phases, was a case launched in 1999 by a group of environmentalists against the United States Bureau of Reclamation and the United States Army Corps of Engineers alleging violations of the Endangered Species Act and the National Environmental Policy Act.

The case resulted in significant changes to water and river management in the Middle Rio Grande Basin of New Mexico in an effort to reverse the damage that had been done to the habitat of two endangered species.

[2] The waters of the middle section of the Rio Grande in New Mexico, running from north to south past the city of Albuquerque, have been used for irrigation for at least 1,000 years.

In the 1950s the Bureau of Reclamation and Corps of Engineers took over responsibility for rehabilitating, maintaining and operating the storage dams and the river channel.

In 1999 a group of conservationists filed suit against the Bureau of Reclamation and the Corps of Engineers on the grounds that they had failed to adequately consult with the United States Fish and Wildlife Service, as required under the Endangered Species Act, to determine if action should be taken to avoid jeopardizing the minnow.

[5] However, irrigation and felling of trees upstream in Colorado added silt to the river that was deposited when the current slowed to the north of Albuquerque.

The Bureau of Reclamation undertook extensive work on the river channel, straightening and strengthening the banks and clearing the floodway.

Invasive species such as Russian olive that are adapted to the drier, more stable environment began choking out native trees and plants.

[14] The southwestern willow flycatcher breeds in dense riparian habitats along rivers, streams, or other wetlands, including the Rio Grande near San Marcial.

Where practical, the Biological Opinion must define Reasonable and Prudent Alternative actions to avoid jeopardizing the endangered species.

The Fish and Wildlife Service received a court order to accept the Department of Interior's Rio Grande silvery minnow Recovery Plan and to conduct an Environmental Impact Statement for this stretch of the river.

[18] The Defenders of Wildlife, Forest Guardians, National Audubon Society, Sierra Club, and other environmental organizations filed suit in 1999 on behalf of the Rio Grande silvery minnow (Hybognathus amarus) and the Southwestern willow flycatcher (Empisonax trailii extimus) against the Bureau of Reclamation and the Corps of Engineers for failure to fully consult with the Fish and Wildlife Service.

The environmental groups made the case that the Bureau of Reclamation and the Corps of Engineers had "significant discretion over virtually all aspects of their funding and operation of the Project, and therefore they must consult with the Fish and Wildlife Service on all of these actions.

[19] It emerged in the hearings that the Middle Rio Grande Conservancy District had been using 11.36 cubic feet of water for each square foot of irrigated land.

The Environmental groups filed a second amended complaint in which they contested the validity of the Biological Opinion while repeating their claim that the Bureau of Reclamation and Corps of Engineers had not consulted with the Fish and Wildlife Service to the fullest extent of their discretionary authority.

[21] However, the court found that the Bureau of Reclamation had discretion over its actions, so the Endangered Species Act required it to consult with the Fish and Wildlife Service.

They asked that the court order the federal agencies to release the water needed to meet the flow requirements defined in the 2001 Biological Opinion.

On 12 September 2002 the Fish and Wildlife Service issued a new biological opinion which agreed that the Bureau of Reclamation operations probably jeopardized the minnow, but said there was no "Reasonable and Prudent Alternative".

In this Biological Opinion the Fish and Wildlife Service concluded that proposed actions by the Bureau of Reclamation and Corps of Engineers, whether or not they were discretionary, would probably jeopardize the continued existence of the Minnow.

The Fish and Wildlife Service defined Reasonable and Prudent Alternatives "based on biological needs of the species, independent of sources of water and discretionary authority."

[24] The Court of Appeals quoted the attorney for the plaintiffs-appellees, who called the silvery minnow the equivalent for the Rio Grande of a canary in a coal mine, an essential indicator of the health of the ecosystem.

The Bureau of Reclamation had published a plan to implement the measures defined in the Biological Opinion, assuming they were allowed to use water for this purpose.

The environmental groups then sought to withdraw their motion to dismiss, saying their scope-of-consultation claim was not mooted by intervening events because the violation was likely to recur.

The court said that when the Fish and Wildlife Service issued the 2003 Biological Opinion and the Bureau of Reclamation adopted it, they had acted voluntarily.

Any question about whether the Bureau of Reclamation and Fish and Wildlife Service would in fact consult again in the event of some future change was too speculative to be considered.

A number of projects are being undertaken to restore the silvery minnow's habitat, including a study of ways to allow the fish to pass the San Acacia Diversion Dam.

(a) Notwithstanding any other provision of law and hereafter, the Secretary of the Interior, acting through the Commissioner of the Bureau of Reclamation, may not obligate funds, and may not use discretion, if any, to restrict, reduce or reallocate any water stored in Heron Reservoir or delivered pursuant to San Juan-Chama Project contracts, including execution of said contracts facilitated by the Middle Rio Grande Project, to meet the requirements of the Endangered Species Act, unless such water is acquired or otherwise made available from a willing seller or lessor and the use is in compliance with the laws of the State of New Mexico, including but not limited to, permitting requirements.