WASHINGTON  The Environmental Protection Agency revoked the permit for one of the nation’s largest mountaintop-removal coal mining projects on Thursday, saying the mine would have done unacceptable damage to rivers, wildlife and communities in West Virginia. It was the first time the agency had rescinded a valid clean water permit for a coal mine.

Arch Coal’s proposed Spruce No. 1 Mine in Logan County, which would have buried miles of Appalachian streams under millions of tons of residue, has been the subject of controversy and litigation since the first application was filed more than a decade ago. Opposition intensified after the Bush administration approved the mine’s construction in 2007, issuing a permit required under the Clean Water Act.

The boldness of the E.P.A.’s action was striking at a time when the agency faces an increasingly hostile Congress and well-financed business lobbies seeking to limit its regulatory reach. Agency officials said that the coal company was welcome to resubmit a less damaging mining plan, but that law and science demanded the veto of the existing plan.

Environmentalists welcomed Thursday’s decision. But the mining company and politicians in West Virginia expressed fury, saying the action was an unprecedented federal intrusion, an economic catastrophe for the state and a dangerous precedent for all regulated industries.