A $27 million federal study of the Chesapeake Bay is turning up evidence of long-term pollution and dwindling marine life and setting off calls for new measures to protect America's preeminent estuary.

Scientific data point to several trends, chiefly in the bay's upper region above the Chesapeake Bay Bridge: Suffocating phosphorus and nitrogen are pouring into the bay; toxic metals and hazardous synthetic chemicals are piling up, and striped bass and other key fish species, bay grasses and other aquatic life have sharply declined.

"If we wait 20 more years and do all the research necessary to prove this without a shadow of a doubt, then it may be too late to reverse the situation," said Kent S. Price, a marine biologist from the University of Delaware working in the Environmental Protection Agency study. Price said he once considered the bay pristine. "I don't think so anymore."

Federal officials, concerned about possible controversy, are quick to point out that conclusions are still being drafted. "We haven't released any findings yet, tentative or otherwise, that have gone through peer review," said Peter N. Bibko, administrator of EPA's Middle Atlantic region.

The bay, scientists note, remains cleaner and less disturbed than many American estuaries, which are partly enclosed inlets where salt water from the ocean mixes with fresh water from rivers and streams. But data compiled by more than 100 university and government researchers in the six-year EPA project point to widening deterioration.

With the study still half a year from completion, bay advocates are already pressing for more federal money and "remedial action" by Maryland, Virginia and Pennsylvania officials. Pennsylvania figures in the debate because the Susquehanna River, which flows through the state, is the bay's largest tributary and, according to some evidence, a major source of pollution.

Possible measures to preserve the bay may include controversial farming techniques to curb phosphorus and nitrogen discharges, costly improvements in sewage treatment plants and industrial pollution controls. Sen. Charles McC. Mathias Jr. (R-Md.) is pushing for a $2 million appropriation to continue scientific monitoring. Other bay advocates are urging the Reagan administration not to end the sizable federal role in safeguarding the bay.

Formed 10,000 years ago when the Atlantic Ocean drowned the ancient Susquehanna Valley, the bay is the largest estuary in the contiguous U.S. It is traversed by shippers using the ports at Baltimore and Hampton Roads, commercial fishers and seafood dealers, recreational boaters and hunters, marine researchers and environmentalists.

For decades, industries, farms and population centers adjoining the bay and its tributaries have left a deepening imprint on its bottom sediment, water quality and wildlife, as the new research data demonstrate.

"The annual average concentration of total nitrogen and total phosphorus has approximately doubled since the early 1960s in the upper bay," said Virginia Tippie, a University of Rhode Island oceanographer taking part in the study. Excess phosphorus and nitrogen may lead to damaging growth of tiny organisms that deplete supplies of dissolved oxygen needed for marine animals and cut off light essential for submerged grasses.

Metals, many of them considered toxic, have gradually built up in the bay's sediment over decades of industrial growth, according to sediment analyses. This long-term accumulation of metals, which may be taken in by shellfish and other organisms, has prompted concern partly because the sediment tends to remain trapped in the upper bay and does not get washed out to sea. In at least one water sample, the concentration of cadmium in the bay was found to be higher than that likely to kill fish larvae.

Robert Huggett, a chemical oceanographer at the Virginia Institute of Marine Sciences, has reported a substantial buildup of suspected cancer-causing substances in sediments especially in the upper bay. "Apparently they're increasing because of the increased use of fossil fuels," he says. The substances are emitted by coal-fired electric power plants, automobiles and other sources of fossil-fuel combustion.

Aquatic grasses, a primary index of the bay's health, declined markedly in recent years. Government surveys found these grasses covered 19 percent of key sites on the bay in 1971, but only 4 percent in 1979. "It's been pretty much downhill ever since the late 1950s and 1960s," said J. Court Stevenson, a botanist at the University of Maryland's Horn Point Environmental Laboratory near Cambridge.

Laboratory experiments have shown that concentrations of nitrogen and phosphorus similar to those found in the bay may severely damage the grasses, Stevenson noted. "As far as cause and effect, I think it's emerging very clearly." Apparently the chief factor, he said, is that increased phosphorus and nitrogen promote the growth of tiny organisms on the plants' leaves, sharply reducing the amount of light available to the grasses.

Matthew C. Perry, a wildlife biologist for the U.S. Fish and Wildlife Service, links the decrease in grasses to departures from the bay of many ducks, chiefly pintails, wigeons and redheads. His study provides "a strong indication that it's the degradation of the winter habitat that's affecting the bird," Perry said.

Steep declines have been noted in the bay among several species of fish that spawn in fresh water, including striped bass, shad, white perch and alewife. The amount of striped bass, or rockfish, caught by commerical fishers in the bay dropped from 7.3 million pounds in 1973 to 2.5 million pounds in 1980, according to government statistics. Researchers say oysters have also decreased markedly in the bay since the 1950s and that oyster young declined significantly in the last decade.

Scientists are now studying these overlapping trends to determine how closely they are interconnected, an extraordinarily complex issue. Each plant and animal species, researchers note, may be affected in different ways by factors ranging from seasonal fluctuations, such as rainfall or drought, to human enterprises, such as dam building and discharges of pollutants.

Similarities in where these trends occur seem, however, to suggest some link between declines in marine life and increases in phosphorus, nitrogen, metals and other pollutants, some researchers say. A computer study is expected to provide further statistical evidence.

Scientific studies are complicated, moreover, because not all evidence points to deterioration. The lower portion of the Potomac River, a bay tributary, appears cleaner than in the past, apparently because of improvements at the Blue Plains sewage treatment plant. Buildups of toxic substances in the bay's sediment may have been somewhat less severe in recent decades, researchers say, than during World War II.

Several species of fish that spawn in salt water, such as bluefish and menhaden, have increased in the bay, apparently replacing those that spawn in fresh water. Some waterfowl also adapted to the loss of bay grasses by changing their feeding habits, biologists say.

Nevertheless, bay advocates express mounting worries, notably about findings suggesting the Susquehanna's impact. "This is what puts the finger on Pennsylvania as a key in the saving of the bay. Those of us below them are at their mercy," said John S. Gottschalk, a retired U.S. Fish and Wildlife Service chief who now is president of the Citizens Program for the Chesapeake Bay.

Millions of pounds of phosphorus and nitrogen enter the bay annually from the Susquehanna, scientists say. Jack Hartigan, a Northern Virginia Planning District Commission official, said his computer study shows that the Susquehanna picks up most nitrogen and phosphorus through runoff and ground water drainage from agricultural fields. The two substances are components of fertilizer.

But Pennsylvania officials contend the Susquehanna has already undergone a substantial cleanup and reject complaints by bay advocates as premature and possibly unfair. The Susquehanna "is an excellent-quality stream," said Theodore P. Clista, a Pennsylvania Water Quality Management Bureau official. "The question is 'Who did what as far as control measures to this point in time and did everybody do their fair share?' . . . You have to establish some basis of equity here."

In farm areas, researchers suggest phosphorus and nitrogen discharges into waterways may be reduced by a shift from traditional plowing to new limited-tillage techniques designed to prevent excessive soil erosion. In urban areas, costly drainage basins to catch storm runoff might be required along with advanced sewage treatment. Industrial antipollution measures may be considered, officials say, to stem discharges of metals and other toxic substances.

No federal money has been set aside for the bay study after current EPA allotments run out in January, and government officials and conservationists are debating the issue. EPA administrator Bibko said the agency has "not ruled anything out" and may consider some additional spending. "Let's see if the states are willing to put up as well as EPA," he added Others are less sanguine.

About $200,000 a year is needed to operate the computer system set up as part of the EPA study, officials say. Additional funds may be sought for monitoring and research. "We're sorry to see a big EPA emphasis on the Chesapeake Bay come and go with no follow-through," said William C. Baker, executive director of the Chesapeake Bay Foundation, a conservation group. "To just drop it now would be so unfortunate."