Washington — The head of the nation's toxic waste program was nominated Thursday to fill the shoes of EPA administrator William Ruckelshaus. President Reagan chose Lee M. Thomas, assistant administrator in charge of the Superfund program, for the No. 1 spot at the Environmental Protection Agency. If approved, Mr. Thomas will be assuming a job that many observers call one of the toughest in government.
Although Ruckelshaus, who announced his resignation Wednesday, insists he is leaving for personal reasons, he has in recent months talked about his job with much frustration.
Intramural policy fights, particularly with budget chief David A. Stockman, were but one of Mr. Ruckelshaus' problems. The cleanup jobs EPA now faces, such as toxic dumps, are far tougher than those it tackled during his first turn at the agency, in the early '70s.
Congress shows no sign of breaking its deadlock over major environmental laws , many of which have expired and need reauthorization. Environmentalists, polarized by early Reagan administration actions, were wary of Ruckelshaus' intentions.
''Eighty percent of what we do we get sued on,'' Ruckelshaus said to a small group of reporters earlier this month. ''Eighty percent! That's terrible!''
The tall, genial Ruckelshaus sent President Reagan a resignation letter Wednesday, catching much of official Washington by surprise and many environmentalists out of town. At the same time EPA confirmed that deputy administrator Alvin Alm was also departing.
An EPA official close to Ruckelshaus insists the director's decision was a straightforward desire to return to the private sector.
''There are elements of frustration in the job,'' the official says. But in talking about the difficulties of running the EPA, Ruckelshaus ''has been trying to educate people where the environmental movement is today. Things are a lot more complex than they used to be.''
Ruckelshaus has lost none of his appetite for government service, the official adds. ''I got in at 6 this Monday morning. Bill was right on my heels, at 6:15.''
In the 20 months he spent at EPA, Ruckelshaus did much to clean up the damage done by his predecessor, Anne Gorsuch Burford, observers say. He brought in dozens of talented people to replace Burford appointees; he brought agency purchasing power back to pre-Burford levels. Morale at the agency, which had been lower than a basement floor, quickly rose.
He has stepped up enforcement efforts for clean air and water laws, gotten the Superfund program for cleaning up waste dumps moving again. But he has either not wanted or been unable to launch an acid rain cleanup program, or to ask for more Superfund money.
''For the most part he did a very good job,'' says William Becker, director of an association of state air-pollution officials. ''He has been open with us, and honest, even though we didn't always agree.''
''But I could sense his frustration,'' Mr. Becker adds, ''primarily with OMB.''
David Stockman, director of the Office of Management and Budget (OMB), was a particularly tough opponent for Ruckelshaus, who, after years at EPA, the Justice Department, and the Federal Bureau of Investigation, is no slouch himself at political infighting. At a Cabinet Council meeting last year, Mr. Stockman pulled out charts aiming to show that a Ruckelshaus acid-rain cleanup would cost thousands of dollars per fish life saved, thus defeating the plan.
A number of environmentalists, in fact, speculate that this sort of intramural battle is what caused Ruckelshaus to resign. Some even say the EPA chief was forced out by an administration that no longer needs to appear as if it was softening on environmental matters.
''Ruckelshaus is an advocate of policies inconsistent with (those of) the White House,'' says Jonathan Lash, an lawyer for the Natural Resources Defense Council, a group that often sues EPA.
Mr. Lash says he will be watching the coming budget: If it contains big cuts in EPA funds, it will add to his belief that Ruckelshaus was shown the door.
As things stand now, ''he leaves behind little of permanence,'' Lash says.
Ruckleshaus ''had good intentions,'' adds a Sierra Club spokeswoman. But ''he was very loyal. In many instances (such as acid rain) he was the fall guy for the administration.''
Congressional reaction to the resignation was mixed, for the most part falling along party lines. Rep. John Dingell (D) of Michigan, chairman of the Energy and Commerce Committee, charged that Ruckelshaus had been fired.
Sen. James Stafford (R) of Vermont, chairman of the Environment and Public Works Committee, said in a statement that he regretted Ruckelshaus' departure. ''I had hoped he might stay another two years, in order to make another major effort to move badly needed environmental laws.''