The Chesapeake Bay has in recent years been one of the most studied and talked about natural phenomena in the country - but according to bay experts the estuary is still shrouded in mysteries that endanger it.

A three-day conference of the scientific, government and citizen experts, sponsored by the Chesapeake Research Consortium at the Patuxent Naval Air Station in St. Marys County, concluded that there is plenty of reason to worry about the Bay but no reason to panic.

Environmentalists, scientists and lovers of the Bay have become increasingly concerned in recent years about the fate of the Bay, the largest and richest estuary in America. It provides food, fun and energy for many of the 8 million people who live in its region and perhaps 17 million in its watershed.

A listing of the problems and afflictions of the Bay sounds like a watery Armaggedon: millions of gallons of human sewage are pumped into the Bay every day; thousands of gallons of oil end up in the Bay every year; toxic chemicals of many kinds and unknown quantities leak into the Bay from offshore runoffs; vast amounts of siltation must be dredged from the big boat channel that splits the Bay lengthwise and dumped somewhere, and soon liquefied natural gas, one of the most hazardous of substances, will be shipped into the bay to Cove Point.

Much vegetation is disappearing from the bay, reducing the food available to bay life, and the bay life itself is available to watermen and sport fishermen in smaller quantities.

Oysters are in short supply. Some scientists think they aren't reproducting. Others think the reproduction process is proceeding normally but that something is happening to the oysters before they mature. James E. Douglas of the Virginia Marine Resources Commission said: "What about that bottom paint most people put on their boats? It's toxic in order to keep the boats clean. Are oysters being killed by it? I don't know; I'm just asking."

Rockfish are in low supply because they "haven't spawned effectively since 1970," said L. Eugene Cronin, one of the organizers of the conference. "Ducks are in serious trouble," he said. "Where we had them in the hundreds of thousands, we've got them in the tens of thousands."

Cronin, speaking for a research group organized to sum up the bay's status for the conference, said the bay faces three major problems: The substantial chemical pollution, which is largely a mystery; the oyster shortage, also a mystery; and the decreasing amount of vegetation, no less a mystery.

Therefore, Cronin said, despite all the studies by various organizations, despite all the scientific research data, more information is needed.

It will come in large part from the sponsors of the conference, The Chesapeake Research Consortium, which is another way of saying Cronin, William J. Hargis Jr. and Donald W. Pritchard - a scientific troika that has built the three main research groups in the bay.

For two decades, Cronin was head of the University of Maryland's Chesapeake Biological Laboratory and is now associate director of its Center for Environmental and Estuarine Studies.

For most of the years since the Virginia Institute of Marine Science was founded in 1940, Hargis has been its director.

Donald W. Pritchard founded the Chesapeake Bay Institute at Johns Hopkins Unversity in Baltimore in 1948 and was its director until illness caused him to step down a couple of years ago. He now is doing oceanographic research.

The three formed the Chesapeake Bay Research Council 12 years ago to formalize cooperation of scientific endeavor and exchange of information.

Later the group linked up with the Smithsonian Institution and formed the Chesapeake Research Consortium to receive financing from the National Science Foundation for research.

Now there are scores of scientists with millions of dollars and a flotilla of boats representing the consortium in research.

At the conference Sen. Charles Mc. Mathias (R-Md.) again suggested his plan for a Chesapeake Bay commission that would function as an overall administrative clearinghouse under a federal law that requires initiative from the states.

And Lt. Gov. Blair Lee of Maryland said that although in the past "state leaders as a species have tended to get nervous or almost paranoid at any suggestion of a federal presence," Maryland was willing to consider positive proposals about the bay.

Virginia's Douglas, in an interview said, however, that his state still was standoffish about the proposal and he was "almost paranoid" about suggestions of a federal presence.