Seeking to bring federal regulations in line with a 2001 Supreme Court ruling, the Bush administration in January took the first step toward removing federal protection from millions of acres of wetlands.

The federal action, jointly announced Jan. 10 by the EPA and the Army Corps of Engineers, directs field staff not to assert federal jurisdiction over isolated wetlands that are intrastate and nonnavigable unless first getting approval from agency headquarters.

In addition to offering the new guidance to staff, the agencies announced they were soliciting comments for new rules that will formally define what wetlands are exempt from regulations.

The guidance was in response to a January 2001 Supreme Court ruling in an Illinois case which said the federal government could not regulate activities affecting an isolated pond where the only connection to other navigable waterways was its use by migratory birds.

Since that decision, federal regulators had interpreted the rule narrowly, saying completely isolated waters only lost federal jurisdiction when migratory birds were the only connection with other waterways.

The administration’s action in January essentially extended the exemption to all isolated wetlands, many of which were still being regulated because of their links to recreational use and other forms of interstate commerce.

“There was a court decision that asked for a minor adjustment in interpretation that could have been done with a tack hammer, and they used a sledgehammer to fix the issue,” said Bob Ferris, vice president of the Chesapeake Bay Foundation.

No one knows exactly how many acres of wetlands are affected regionally or nationally, although the EPA has estimated that the change might affect about 20 percent of the nation’s 100 million wetlands.

Regional EPA officials were still trying to assess the impact in the Bay region, but it appeared likely, based on a 2000 analysis completed in Virginia, that hundreds of thousands of acres of wetlands could be exempted from federal regulations.

The report, by the Virginia Institute of Marine Science, identified about 1.27 million acres of wetlands in the state, of which between 180,000 and 411,000 acres could be considered as “isolated” depending on the methodology used.

That doesn’t mean the wetlands would be vulnerable: All states in the watershed except Delaware have programs to regulate wetlands.

The action would remove the federal regulatory backstop that has existed if states were to revise their programs, and could increase the burden on state regulatory agencies.

Isolated wetlands are important because they help to recharge groundwater supplies, and they provide important habitat for a variety of wildlife. They are especially important for amphibians, whose populations are in sharp decline, because the separation from other waterbodies helps to protect them from predators.

Federal officials said the change was necessary because of the questions raised by the Illinois case and other decisions about the federal role over nonnavigable waterways that are not used in interstate commerce.

Further, they said some of the wetlands would still be protected by other federal programs, or state regulations.

They noted that the vast majority of wetlands would continue to receive federal protection. “We are committed to protecting America’s wetlands and watersheds to the full extent under the Clean Water Act and the recent Supreme Court ruling,” said EPA Administrator Christine Whitman.

Environmentalists, though, are worried that the exemption could become wider. The EPA and the Corps also announced they were seeking input to shape new rules that will further guide where federal jurisdiction over wetlands should apply.

The agencies said they were seeking input from scientists, the regulated community and others. The agencies also said they were evaluating whether the court ruling could impact other Clean Water Act programs affecting isolated waterbodies, such as those that require permits to discharge pollutants.

Environmentalists said those waters are still linked to other waterbodies through groundwater, and the new actions ignore 30 years of Clean Water Act interpretation that all waters should be protected.

“The Bush administration’s proposal ignores basic hydrology, because pollution in streams and wetlands eventually flows into big rivers and causes more pollution downstream,” said Joan Mulhern, senior legislative counsel for the environmental group Earthjustice. “And it ignores the law, since the very purpose of the Clean Water Act is to eliminate pollution where it begins rather than forcing huge cleanup expenses on communities who depend on clean waterways for fishing, swimming and drinking water.”

The Chesapeake 2000 agreement calls for achieving a no-net-loss of existing wetland acreage and function within regulatory programs. It also calls for restoring 25,000 acres of wetlands in the watershed.