Environmental Protection Agency Administrator Lee M. Thomas said yesterday his agency would continue its strong support of efforts to clean up the Chesapeake Bay, adding that the project could be a model for cleaning up other polluted bodies of water across the nation.

After completing his first tour of the bay since taking over the EPA in February, Thomas said he considers the bay "an important national resource" and pledged to continue EPA projects begun by his predecessor, William D. Ruckelshaus.

Thomas joined Interior Secretary Donald P. Hodel, Maryland Gov. Harry R. Hughes, Virginia Gov. Charles S. Robb, Sen. Paul S. Sarbanes (D-Md.), District of Columbia Deputy Mayor Thomas Downs and other federal and state officials on a tour of the Chesapeake organized by Sen. Charles McC. Mathias (R-Md.).

"Significant progress has been made in the past two years," Mathias said of the bay. "But we have to understand that it's going to be a long haul."

The bay cleanup received $13.2 million in federal funds in fiscal 1985, $10 million of which came from the EPA. EPA funds are used by the states involved in the cleanup to tackle such problems as finding ways to alleviate soil runoff from farms. The administration has requested another $10 million for the EPA in fiscal 1986.

Thomas' expression of continued EPA support was welcome news to cleanup supporters, who feared that the departure last November of Ruckelshaus, the Chesapeake's most influential champion in the Reagan administration, would jeopardize some of the programs.

Ruckelshaus was widely credited with overcoming opposition from the Office of Management and Budget, which last year opposed spending so much money on the program. Thomas said EPA officials believe the funding process worked out between the agency and the states involved in the Chesapeake cleanup can be used on bodies of water elsewhere, such as the Puget Sound in Washington state.