Michael S. Haire crouched over the square foot of mud he had scooped from the bottom of the Patuxent River, ran two fingers lightly across the sample and held the chocolate-dark ooze to his nose.

"No odor," said Haire, a marine expert with the Maryland Office of Environmental Programs. "That's not a bad sign."

There's no glamour in smelling mud, but it's all part of the war on pollution in the Patuxent River, a waterway stretching 110 miles from western Howard County to this tiny island at the Chesapeake Bay.

Menaced by wastewater treatment plants in Howard and Prince George's counties and by fertilizers washing off the tobacco fields of Calvert, Charles and St. Mary's, the Patuxent is a river on the brink, a fragile ecosystem that Haire and others are trying to save through an ambitious program of scientific tests, tougher waste control laws and new farming methods.

"Oyster production in the river is way down, fisheries are off and the clarity of the water has diminished in recent years," said Haire, one of 10 state and federal scientists who last week were aboard the Discovery, a 45-foot trawler crammed with enough gear to outfit a large laboratory. "OEP has no higher priority than the cleanup of this river."

Haire is one of the leaders of a $430,000, three-year program to take the pulse of the Patuxent, to pinpoint those stretches of the river most contaminated by waste and fertilizers. The study, called a "nutrient-flux survey," may be the key not only to the Patuxent's future, but to the Chesapeake Bay's as well, officials said.

"That, of course, is the larger question," said OEP Secretary William M. Eischbaum. "What happens to the Patuxent is in a lot of ways going to be reflected in the bay."

"This is big test for us," said Haire, an affable, shaggy-haired New York native who grew up on Long Island Sound.

"If we succeed here, it could make the difference in the quality of the bay 10, 20, 50 years from now."

The Discovery's crew will spend the rest of the year testing mud, marine life and river water for traces of phosphorous and nitrogen, two nutrients that feed the estuary's microscopic algae--which in turn rob the water of the oxygen that keeps fisheries and shellfish beds alive. Nitrogen and phosphorus drift downstream from wastewater plants such as the Savage facility in southern Howard County and Prince George's Western Branch plant, which account for roughly 22 million of the 36 million gallons of wastewater pumped into the Patuxent daily.

The Discovery's mission is important to the Patuxent's health, Eischbaum and Haire said, simply because it marks the first time the state has measured nutrient levels. "The Discovery will set the benchmark," said Haire, peering into the dark-green river near St. Leonard's Creek. "From here on in, will be able to get a pretty good idea of how the river's doing. We couldn't do that before."

The ultimate cost of of the Discovery's research, which will help officials set farming-fertilizer controls and emission safeguards at wastewater plants, will be high, Eischbaum said. Under a cost-sharing program approved two years ago by the General Assembly, the state will spend $5 million alone trying to convince farmers to use new tilling and fertilizing methods to reduce the nutrient-rich silt washing into the river.

At the Western Branch and Parkway waste plants, meanwhile, the cost of installing nitrogen controls could run as high as $18 million, officials said. Maryland is prepared to spend that amount if the U.S. Environmental Protection Agency withholds the money, Gov. Harry Hughes announced recently.

"We're trying to get on the right course with the Patuxent," Eischbaum said. "But we may not even see our first increment of progress until 1987."

Studies like the one being conducted by Discovery's crew of biologists, engineers and marine experts make good public relations for government officials who have for years battled local environmentalists over the quality of the Patuxent.

"For a long time, the public view was that it wasn't important to us what happened to the Patuxent," Eischbaum said in an interview this week. "But we're taking the steps now. . . . "

For activists such as Marilyn Reeves of Laurel, who has called for a cleaner Patuxent for more than 20 years, the nutrient control and study program comes not a moment too soon.

"A Patuxent cleanup? Why, things have been at a standstill since late '81," Reeves said.

In that year, a coalition of politicians, environmentalists and local groups met in northern Howard County to draft a plan to protect the Patuxent's resources.

"The state does not have an adequate monitoring program," said Reeves, who lives near the river. "No one is saying, 'Yes, the Patuxent is going to be protected--all 110 miles of it.' "

"You just don't sit back and wait till you have every concrete fact at your disposal," said Haire, after a morning on the Discovery, "but the research on what's happening to the river is essential.

"We've gone from pie-in-the-sky, Jacques Yves Cousteau-y kinds of programs to very pragmatic programs. In the short run, we may be remaking the way we think about the Patuxent."