ON MOST ISSUES President Reagan has pretty well had his way with Congress.

On environmental issues he has not. The administration tried in his early years to rewrite the major environmental laws to reduce their burden on business. Environmental groups and key figures in Congress resisted. The result has been an awkward standoff in which few bills have been passed in either direction. As the laws conferring regulatory authority have come up for renewal, Congress has merely extended them year by year through the appropriations process.

Now, however, this may be changing. The Senate easily passed last month, over administration objections, a major new bill to protect the supply of drinking water. A similar bill awaits floor action in the House. Committees in both houses are at work on bills to extend and expand the Superfund program for cleaning up hazardous waste dumps, which expires this year. And on Thursday the Senate passed, 94 to 0, a bill that the administration also opposes, extending and strengthening the Clean Water Act. Last year the House passed a similar bill 405 to 11, only to see it die in the Senate. This year a bill has cleared House committee.

For the most part, the Senate clean-water bill would preserve and fine-tune current law; in one important way it would broaden it. A new program would deal for the first time with what is known as non-point source pollution, the generalized kind that comes not from particular pipes but entire fields. Half the pollution in the country is of this type. The leading example is runoff from farm fields that have been covered with pesticides and fertilizer.

Among many other provisions, the bill would also prevent in most cases the degradation of water now cleaner than the law requires; limit the power to grant waivers from industry-by-industry clean- up requirements; and require extra efforts, beyond even installation of "best available" clean-up technology, in some areas that are especially polluted. Factories in such areas might have to limit their operations.

The administration opposes all these provisions except the one about water cleaner than the law requires. It opposes even more the other half of the bill, which authorizes continued federal funding of state and local sewage treatment plants. The funding was begun in 1972 to help state and local governments meet the higher standards of the Clean Water Act, then just passed. For both fiscal and federalism reasons, the administration now wants the responsibility returned to the state and local level. The bill would not do that until the 1990s.

A letter last week from Environmental Protection Agency Administrator Lee M. Thomas to Senate Majority Leader Robert Dole warned that the bill, "if enacted in its present form . . . would not be in accord with the program of the president." But if that is a veto threat it seems a weak one. A 94-to-0 vote in the Republican-controlled Senate is a pretty plain message. The politics of the environment seem to have come unstuck, and in a healthy way.