The Chesapeake Bay has lost 16 percent of its valuable marshland in three decades to federally subsidized farm irrigation and drainage projects, a U.S. Fish and Wildlife Service biologist said today.

The projects supported under a 1954 law by the U.S. Soil Conservation Service provide "short-term benefits to a few individuals but long-term adverse environmental impacts," said Timothy N. Hall, a biologist who works in Annapolis for the federal wildlife agency.

The battle lines were drawn here today as 250 scientists, bureaucrats, environmentalists and others debated the causes behind the loss of valued wetlands, the marshy and swampy areas that border the bay.

Long cherished as a natural habitat for waterfowl, wetlands also act as a filter, preventing life-choking chemicals and run-off from inland farms and developments from going into the bay.

The conference, organized by the Washington-based Environmental Law Institute, is being held at a time of heightened public awareness and governmental concern about the future of the Chesapeake.

Maryland instituted a ban this year on fishing for rockfish, also known as striped bass, because of a serious decline in the species. Similarly, the oyster harvest from the bay continued its long-term decline this winter.

The three-day conference is entitled, "Wetlands of the Chesapeake -- Protecting the Future of the Bay." But not everyone agrees on how to save the vanishing marshes or even on the reason for their decline. The tensions were apparent as those from different disciplines convened at the tony Tidewater Inn in this, the waterfowl capital of Maryland.

"Agriculture will always be a major industry on the Eastern Shore," said Hall, the biologist, "but the old way of doing business may no longer be the proper way."

Hall said that 3,200 acres of Chester River wetlands in Maryland and Delaware could be altered or destroyed by federal and state farm drainage proposals now pending. The purpose of the proposals, he said, is to irrigate and drain more land to maximize crop yields. But the effect will be an increased nitrogen and phosphorous load in the bay, he said.

"You're never going to stop agricultural drainage, at least in my lifetime," Hall said. "But the economic analysis is not there to show a substantial benefit in yields before and after channel work . . . . We can't await the research and watch our resources continually decline."

Hall's view was challenged by J. Wendell Gilliam, a professor of soil science at North Carolina State University. "You can have drainage and high-quality water," he said. "There's no way environmental people, soil specialists and farmers can fight. We're going to have to live together. We can live together."

Some participants questioned whether wetlands and agriculture as now practiced could coexist. Charles R. Lee, an Army Corps of Engineers official, assured the gathering that they could if farmers were willing to spend money for certain technological measures.

But precisely what the public wants, at least one speaker suggested, is debatable. Many people aren't concerned with wetlands, said Erwin Garskof, who works for the Corps of Engineers enforcement branch in Pennsylvania. "They'd rather have a lawn than a wetland."