Exempting headwater streams and isolated wetlands from federal protection would have “significant impacts” on fish, wildlife and water quality throughout the nation, according to an analysis by the U.S. Fish and Wildlife Service.

The service, the main part of the U.S. Department of Interior which deals with wetlands, said rule making being considered to reduce Clean Water Act jurisdiction was “more broad than necessary” to comply with a recent Supreme Court decisions.

The service said that protecting all wetlands was essential to the Act’s goal to “restore and maintain the chemical, physical and biological integrity of the nation’s waters.” And it suggested that loosening the protections could result in the additional loss of more than 100,000 acres of wetlands per year.

But those comments never made it to the EPA or the Army Corps of Engineers, the two federal agencies considering a rewrite of the Clean Water Act rules.

The Department of Interior scrapped the service’s analysis and instead submitted comments which called for the federal government to eliminate its oversight of any “isolated, intrastate, non-navigable waters”—exactly the opposite what its own Fish and Wildlife Service biologists recommended.

“It is the prerogative of the department to do that,” said department spokesperson Hugh Vickery. “The secretary of the interior is over the Fish and Wildlife Service. The department has the call. It can make decisions as to exactly what is going to be said by the department.”

In this case, what the department chose to say was sharply different from what was said by its Fish and Wildlife Service.

The comments were generated in response to a request by the Corps and the EPA earlier this year for comments about how to clarify federal Clean Water Act jurisdiction in light of questions raised by a 2001 Supreme Court decision.

In that ruling, the court said the agencies had overstepped their authority when they regulated the filling of isolated ponds where the only connection to other waterways was through the presence of migratory birds.

In its comments, which were forwarded to the Interior Department, the USF&WS said the issue could be resolved simply by not regulating waters where the presence of migratory birds was the only basis for doing so. Any broader interpretation, the service said, could have “significant impacts on valuable fish and wildlife habitats as well as negative impacts to water quality.”

The service contended that the “overwhelming body” of scientific information supports the need to protect “isolated” waters because of their impact on downstream water quality and habitats. Isolated wetlands provide stopovers for migrating birds, temporarily store floodwaters and sediment, and absorb chemicals, improving downstream water quality.

It also said many miles of waterways in the United States are ephemeral or intermittent and under some definitions, could be considered isolated as well. It said streams and wetlands near rapidly developing urban and suburban areas would be “particularly vulnerable.”

The USF&WS estimated that isolated wetlands make up 20–25 percent of the roughly 105 million acres of wetlands in the continental United States. If just 1 percent of the remaining wetlands were lost as a result of reduced jurisdiction, it would result in a 1.1 million acre decline. If that were spread over a decade, the service said, the loss would be 110,000 acres a year, or almost twice the current loss rate of 58,500 acres annually.

In many cases, the service said, state programs would not be able to fill the gap as many of them are prevented from being more stringent than federal regulations. State regulations are also likely to be inconsistent across boundaries. Further, the service said federal biologists may not be able to provide state agencies with comments about impacts to waters where they had no jurisdiction.

It said continued federal regulation was critical to the protection of those areas. While the federal government has programs to help conserve wetlands, “they would be unable to accommodate the large number of wetland basins that could potentially be left without protection.

But the Department of Interior saw things differently. It said “protection of wetlands is an important national goal” but advocated nonregulatory approaches to wetland protection.

“The Department believes that the nation’s wetlands can be protected, and are being protected, by many nonregulatory conservation programs, in which the government provides funds and technical assistance to individuals and organizations for the rehabilitation of both public and privately owned wetlands,” it said in its comment letter.

As of 2000, the department said, nearly 2 million acres had been protected through nonregulatory programs nationwide. That’s a bit less than 2 percent of the nation’s 105 million acres of wetlands.

It argued that the Supreme Court had interpreted the federal jurisdiction narrowly, to exclude “isolated, intrastate, non-navigable waters” and said that the “assertion of a broader interpretation may, under the Court’s decision, run afoul of the limitation on the federal legislative power.”

It cited several examples of federal government support for private efforts to restore and enhance wetlands voluntarily, and said they were the beginnings of a “compelling strategy” to protect wetlands. “If government is to meet its goal of wetlands conservation, it must reach beyond a purely regulatory approach,” the department said.

In its comments, the department also asked the Corps and the EPA for greater exemptions from Clean Water Act regulation for certain forestry practices and for discharges from irrigation ditches.