Two scientists, including President Carter's newest appointee to the Council on Environmental Quality, threw cold, dirty water yesterday on the widely held belief that the Potomac River is being cleaned up.

Robert H. Harris, one of two authors of a 124-page critique of local clean-up efforts, said most of the work to date has been cosmetic. "After you send the corpse to the undertaker, it comes back looking better, but it's still dead," he said.

Harris, the latest addition to the three-member federal council that advises the president on environmental issues, and coauthor Thomas P. Flaherty said efforts to make the river fishable and swimmable are not only failing but wasting millions of tax dollars yearly.

Their conclusions, reached in a study sponsored by the privately funded Environmental Defense Fund for which Harris worked until last month, run contrary to those of many Washington officials, who say the Potomac is getting progressively cleaner.

Last fall, some District officials announced they were ready to recommend the city lift its 50-year ban on swimming in some sections of the river under DC. control. "I think you could create a safe bathing beach" there, said John V. Brink, director of air and water quality for the District.

The Interstate Commission on the Potomac River Basin, a watchdog for the river created by four states and the District, says amateurs and experts it relies on report better fishing and a dramatic reduction in smelly, scummy algal blooms that once fouled large portions of waterway.

"Their [Flaherty's and Harris'] report is contrary to everything we have been hearing and to what I believe has been taking place," said Paul W. Eastman, director of the interstate Potomac River commission.

Even officals of the federal Environmental Protection Agency, which has often been critical of local cleanup efforts took issue with the report.

"Our conclusions are quite a bit different," said Robert L. Collings, an attorney with EPA's Region 3 enforcement branch in Philadelphia, which has jurisdiction over the Washington area. "There has been an improvement in the quality of the river."

One of EPA's top scientists in charge of monitoring the Potomac, Leo J. Clark, said, "If you look at all the data, you could show an improvement in water quality . . . The river is better and we're on the right track in the clean-up."

Flaherty and Harris maintained that EPA and the local area are wrong and have erred in deciding to concentrate on removing one major pllutant -- phosphorus -- and not removing another one -- nitrogen.

Their report is heavily laden with formulas and jargon used by biologists, engineers and computer modelers, but what they say, in essence, is:

Removing phosphorus (a chemical that can promote growth of polluting algal blooms in the river) from sewage is a wasted effort. There is already enough phosphorus imbedded in the Potomac riverbottom to keep blooms growing for at least 40 years, the scientists say. However, the impact of phosphorus-caused pollution can be nullified if nitrogen also is removed from sewage, they say.

Flaherty and Harris say the emphasis on phosphorus results in a daily output of 200 tons of sludge, which is costly to dispose of and has "required 250 acres of land per year for disposal."

Harris acknowledged that thick algal blooms that used to cover the Potomac in the late 1960s and early 1970s have largely disappeared. But he said, they have been replaced by other algae that, though not as thick and smelly, pollute the river, harm aquatic life and keep it as cloudy as "pea soup."

Harris and Flaherty said they based their findings largely on the same data used by EPA's Clark, who says the Potomac is getting cleaner. Clark was philosophical about the different findings. "You give five people the same set of facts, and you are likely to get five different conclusions," he said yesterday.