A bubbling dispute over the Clean Water Act will greet the Environmental Protection Agency's new administrator, who will have to sort out acrimonious differences between his agency and the U.S. Army Corps of Engineers.

The EPA and the corps have never seen eye to eye over a law that requires a corps permit to dispose of material dredged from a body of water or used to fill in a swampy area.

That law is regarded as the government's most powerful tool to prevent the destruction of wetlands, which help maintain water quality by acting as natural filtering ponds and are an important breeding ground for waterfowl and shellfish. The steady rate at which wetlands are being destroyed has alarmed sportsmen, commercial fishermen and wildlife enthusiasts.

But the corps considers the permit process a nuisance, especially since it is required to submit its decisions to the EPA, which weighs them against environmental guidelines to make sure the dredging and filling operations aren't destroying a valuable chunk of wetland.

Assistant Army Secretary William R. Gianelli, in a letter last month to Vice President Bush, argued that the guidelines should not be considered firm rules.

"As long as the guidelines remain as regulatory criteria, Army will be unable to implement fully the task force decision and will be unable to attain optimum management efficiency," Gianelli wrote Bush, who heads a White House task force that targeted the permit program last May as a candidate for regulatory change.

But Bush also got two other letters on the subject.

One was from then-acting EPA administrator John W. Hernandez Jr., who said that what the Army had in mind was issuing permits to projects that would violate the environmental guidelines. Not only would that pose a "significant legal risk," Hernandez wrote, but the administration could "anticipate severe public and congressional reaction."

The reaction wasn't long in coming. The second letter on Bush's desk was from Sen. John H. Chafee (R-R.I.), who said that Gianelli's proposal represented "precisely the type of regulatory excess that is making the public view the Republican Party as anti-environmental."

According to C. Boyden Gray, counsel to the regulatory task force, the dredge-and-fill question has been put on hold until William D. Ruckleshaus has been confirmed as EPA administrator. However, Chafee told Bush in his letter that he intends to bring the matter up at Ruckelshaus' confirmation hearings.

Meanwhile, the corps apparently is attempting to win legislatively what it has been unable to get the EPA to concede. The Cabinet Council on the Environment, headed by Interior Secretary James G. Watt, gave the corps permission last month to draft Clean Water Act amendments and find "a friend on the Hill" to introduce them.

Interior officials declined to explain the apparent contradiction between that action and others Watt has taken regarding wetlands. Watt has called wetland conservation one of his highest priorities and has backed a bill designed to preserve wetlands by forbidding the use of federal funds in any projects that would destroy them.

That bill, however, exempts a long list of projects that affect wetlands, including those undertaken by the Corps of Engineers.