The Environmental Protection Agency and the Interior Department have registered strong opposition to a regional aggreement on tapping the Potomac River to help meet the area's water needs.

EPA, in a report prepared by its regional office in Philadelphia, said plans by the Fairfax County Water Authority and Washington Suburban Sanitary Commission to build water intakes "could seriously impact water quality in the Potamac River and ultimately the upper estuary of the Chesapeake Bay."

"We must recommend that the proposed project be abandoned until adequate safeguards . . . can be established and implemented," the report said.

A letter to the Army Corps of Engineers from theoffice of Interior Secretary Cecil D. Andrus said. "At this time, the department cannot support the agreement . . . until adequate provisions are made to guarantee the establishment and maintenance of a minimum flow in the Potomac River during low-flow periods."

While the two agencies' objections will not necessarily scuttle plans for the two water intakes - a new one on the Virginia side and a replacement on the Maryland side - construction timetables are likely to be delayed. The Corps of Engineers will not grant construction permits until all major environmental issues are resolved.

"The more adverse responces we get, the longer it's going to take," said a spokesman for the Corps of Engineers' district office in Baltimore.

The Fairfax County Water Authority said timing is especially critical for its project. If the authority, which serves more than 600,000 customers in Fairfax and Prince William counties and Alexandria, can't begin construction by this year, its proposed Potomac facility probably wouldn't be ready by the summer of 1981. By that year, the Occoquan Reservoir is expected to be an adequate source of supply.

Last December, the corps, the Fairfax authority and the WSSC, along with the District and the states of Maryland and Virginia, announced they had settled a complicated and protracted controversy on how to share Potamac water in times of drought when river flow is far below normal.

During many months of negotiating and sometimes public bickering, the corps insisted that it would not grant permits for construction of the intakes until there was an agreement assuring the District's water needs during drought. While the suburbs have alternative sources of supply, the District is wholly dependent on the Potomac.

When the regional agreement was signed in January, Fairfax officials hoped that the corps would grant a permit to the water authority as early as April and no later than July.

While the corps could reject the objections of EPA and Interior, that is not too likely. "Generally, the corps abides by our comments," an EPA spokesman in Philadelphia said. "We hope they will this time."

EPA's concern centers on the possibility that in periods of drought, if the suburbs and the District tapped the Potomac to the maximum permitted under their agreement, the river could go dry in places.

Furthermore, EPA said, extensive withdrawal of water during a drought's low-flow conditions would deprive the estuary (that portion of the river between Chain Bridge and the bay) of the fresh water it needs to cleanse itself of sewage effluent. If that happened, EPA said, algal blooms, which choke the river's life, would become "acutely high."

In its generally tough-worded report, EPA said, "Projects which contributed to severe water quality degradation over the extensive areas noted cannot be condoned by EPA."