WITH THE CONGRESSIONAL hearings yesterday, THE STRUGGLE OVER THE Environmental Protection Agency has changed. It is no longer essentially a dispute over who has a right to which pieces of paper. It has moved to all the broad questions of the policies that the agency has been pursuing during the past two years under its present administrator, Anne M. Gorsuch.

Mrs. Gorsuch bitterly accused unspecified environmental organizations of running a partisan campaign of "harassment" against her from the beginning of her tenure. The congressional response was interesting. Mrs. Gorsuch got very little sympathy from either party. On the contrary, the committees seem to be focusing on the extent to which the EPA and Mrs. Gorsuch have departed from the paths that Congress thought it had laid down in legislation.

With the hasty shredding of documents and purging of computer memories, the scent of scandal now hangs over the agency. But the issues between Mrs. Gorsuch and the committees go much farther than access to the records in the toxic dump cases.

Over the past two years, as cost-cutting measures, the agency has discontinued collecting some of the pollution data series. That erodes the base not only for enforcement, but for rational decisions about future protection as well. Under Mrs. Gorsuch, the flow of information and consultation seems to have been severed between the political appointees at the top of the agency and the technical people. One consequence has been an exodus of technicians and scientists, further weakening the agency.

Air and water quality have improved demonstrably over the past decade. But there is some reason to wonder whether the EPA is controlling the right pollutants, and measuring them the right way. The past decade has demonstrated that there are large gains in public health to be achieved, but it is going to take a kind of research and analysis that the agency, under its present leadership, shows no signs of undertaking. These are the questions that lie behind the current quarreling over executive privilege, budget reductions and personnel changes.

When an agency is well managed, it buys itself a substantial degree of discretion in policy. When it is badly managed, it opens itself to challenge not only on its housekeeping but on larger matters as well. When the Reagan administration took office and installed Mrs. Gorsuch at the EPA, it -- and she -- enjoyed for a time the latitude that is granted to every new administration even by those people in Congress who have deep doubts about the direction in which it is headed. That grace period has long since expired or, more accurately, been used up. The events of the past several months now give Congress the strongest reason to look carefully into the internal affairs of the agency. The rumors of misdoing need to be tracked down and either proved or disproved authoritatively.

But common scandal is the least of it. This agency's responsibilities are not trival. The successes and failures of these years will affect the country's death rates for a decade to come.