One-quarter of U.S. lakes, rivers and estuaries remain too polluted for swimming and fishing, the Environmental Protection Agency reported yesterday, four years after Congress had hoped to have the nation's surface waters clean enough for recreation.

The EPA report, submitted to Congress as the latest in a series of biennial water-quality inventories, showed a slight decrease since 1984 in the percentage of lakes and estuaries safe for swimming and fishing. The Clean Air Act set a "national goal" of restoring surface waters to recreational status by July 1983.

Virginia leads the nation in total mileage of unswimmable and unfishable rivers -- 2,232 of its 27,240 miles. Wisconsin and California lead the nation in total acres of lakes considered to have unsuitable conditions.

The report cited "elevated" levels of toxic substances, including cancer-causing chemicals and metals, in 8,500 miles of rivers, 362,000 acres of lakes and 190 square miles of estuaries.

"It is clear from these statistics that pollution due to toxic substances is not a problem that is going away," the report said. "On the contrary, the more we study and monitor for toxics, the more likely we are to find them and realize their pervasiveness."

Rebecca Hanmer, EPA's deputy assistant administrator for water, said the agency has achieved "substantial progress" in remedying the "gross pollution problems that made headlines in the 1970s," such as the demise of Lake Erie. But, she said, increasing amounts of runoff from farms and city streets -- an unregulated form of pollution -- sully surface water and counteract some of the progress in controlling industrial and municipal discharges.

The inventory, based on reports by states, covered a fifth of U.S. river miles, a third of lake acreage and half of the estuarine mileage.

No figure is given for the number of surface water bodies cleaned up under the act. Nor are specific bodies of water cited for violating fishing and swimming standards.

Twenty-six percent of the 370,544 river miles surveyed failed to meet fishing and swimming standards. Thirty-eight states contained polluted portions of rivers and streams.

Of the 12.5 million acres of lakes sampled, 3.4 million acres in 26 states failed to meet fishing and swimming criteria.

A quarter of the 17,600 square miles of estuaries were still considered unswimmable and unfishable. The Chesapeake Bay, according to the report, suffers from high nutrient and bacterial levels, decreasing harvests of fish and oysters.

Toxic substances exceeded state and federal standards in all three categories of surface water, including such cancer-causing substances as polychlorinated biphenyls and the pesticide chlordane. The neurotoxins mercury and lead were found in 24 and 10 states, respectively, according to the report.

In the Great Lakes, the EPA reported a decline in phosphate pollution due to its ban in detergents. But toxic substances were said to still be "widespread."