For the first time, five federal agencies with separate responsibilities for the Chesapeake Bay have made a joint commitment to participate in a multimillion-dollar clean-up of the nation's largest estuary.

At a news conference yesterday on Capitol Hill, representatives from the five agencies signed agreements with the Environmental Protection Agency outlining their responsibilities for the bay cleanup. The agreements signal an unprecedented level of federal involvement in the Chesapeake project.

"This is a historic landmark," said Sen. Charles McC. Mathias (R-Md.), who encouraged the agencies to join hands to clean up the bay. "These agreements symbolize the reversal of years of neglect."

Until this year, the federal government had made only disparate attempts to control the Chesapeake's pollution problems, which stemmed in part from a myriad of regulations affecting the bay and its aquatic life. The lack of coordination among federal agencies and between the federal government and the states emerged in recent years as one of the chief obstacles to a successful war against bay pollution.

Responding to pressure from states, environmental groups, and even from the administrator of the Environmental Protection Agency, William D. Ruckelshaus, President Reagan announced in his State of the Union address this year a $40 million, four-year commitment from the federal government to clean up the Chesapeake. Maryland, Virginia and Pennsylvania also pledged a total of $80 million.

Yesterday's agreements, outlined in principle last summer, require each agency to provide one staff member to handle bay issues, to prepare annual work plans for the cleanup, and to coordinate cleanup activities with other agencies.

Under the Clean Water Act, the EPA is responsible for protecting the nation's water resources, and it will be the pivotal agency coordinating the cleanup. Congress approved about $10 million in the EPA budget for the bay this year.

While Mathias, Ruckelshaus and other supporters of the bay cleanup project hailed the importance of yesterday's agreements -- even celebrating the occasion with a bushel of fresh Maryland oysters served on the half shell -- they cautioned that an unpolluted Chesapeake is still years away.

"It is a very long journey ensuring that the bay is restored," said Ruckelshaus, who is credited as being the prime force within the administration lobbying for the bay project. "On a note of realism, this is a step forward but this journey has many steps."

Sen. John W. Warner, a Virginia Republican, noted the "historic" progress made on the bay cleanup, but added that "the new warfare is the budget." Warner urged Ruckelshaus "to enter that budget warfare" and make sure the administration continues to commit federal funds for the bay.

Bay supporters estimate that the cleanup project could cost as much as $200 million in the next decade.

"I don't know" how much exactly, Ruckelshaus said, when pressed for a specific price tag. "If you put it in one lump you scare people to death."

He added that "changing attitudes and conservation practices" are as important as money in the cleanup effort.

The five agencies that signed the agreements are the Soil Conservation Service, the U.S. Fish and Wildlife Service, the National Oceanic and Atmospheric Administration, the U.S. Army Corps of Engineers, and the U.S. Geological Survey.

The agreements also require the agencies to participate on a joint committee to monitor bay activities, to set up data bases, and to share research and information regarding the bay cleanup.