Administrator William D. Ruckelshaus yesterday fired four top officials at the Environmental Protection Agency, including the heads of the agency's air and water divisions.

Kathleen M. Bennett and Frederic A. Eidsness Jr., assistant administrators for air and water, respectively, submitted their resignations to President Reagan at Ruckelshaus' request, according to agency offi- cials.

Ruckelshaus, acting swiftly on his second day in office to make room for his own management team, also requested and received resignations from the regional administrators in Philadelphia and Boston. The EPA has 10 regions, and two regional administrators, in Seattle and Denver, have already been removed.

EPA sources said that another regional administrator, Sonia F. Crow in San Francisco, also would be asked to resign. But her office said yesterday that Crow, who was out of town and not available for comment, "remains officially the regional administrator."

Twenty high-ranking EPA officials have been ousted since a series of congressional investigations focused attention on the agency earlier this year. In addition to former administrator Anne M. Burford and her deputy, John A. Hernandez Jr., that number includes five of the agency's six assistant administrators, its general counsel and its inspector general.

The latest housecleaning came as the first subpoenas were being served in preparation for a federal grand jury investigation of allegations of impropriety against some former EPA officials.

EPA officials confirmed that subpoenas had been served on employes of the agency's enforcement office.

The Justice Department has been investigating allegations that former general counsel Robert M. Perry committed perjury when he denied, under oath to a congressional panel, knowing anything about "green books" allegedly kept to rate his subordinates' performance.

Other matters expected to come before the grand jury are similar perjury allegations against former hazardous waste official Rita M. Lavelle and Hernandez, as well as allegations of conflict of interest against James W. Sanderson, a former adviser to Burford.

In a related matter, a contempt citation against Lavelle was certified by the House of Representatives and sent to the U.S. attorney's office, which has assigned the case to an investigator.

When Burford was found in contempt last December, the U.S. attorney's office did not assign an investigator, saying it had discretion to decline the case.

Environmentalists who met with Ruckelshaus in April urged him to make personnel changes, contending that the ideological beliefs and industry ties of some officials made them unsuitable for the EPA.

But EPA sources said privately yesterday that Ruckelshaus "agonized" over the fate of some of the officials, particularly Bennett, for whom he reportedly has high regard.

In a statement released by the EPA press office, Ruckelshaus praised Bennett and Eidsness for their "dedicated and professional service" and said both had agreed to serve him as special assistants "until the transitional period we are in is completed."

As a result of the departures, Ruckelshaus will be the only official at the agency who has been confirmed in his job by the Senate. The remaining assistant administrator, research chief Courtney Riordan, was nominated two months ago but has not been confirmed.

The EPA press office said yesterday that Bennett would be replaced on an acting basis by Charles L. Elkins, the air division's policy director, and Eidsness' job will be handled by Rebecca W. Hanmer, his deputy.

The regional administrators removed yesterday were Lester A. Sutton in Boston and Peter N. Bibko in Philadelphia.

In Boston, a spokesman for Sutton said that the resignation was requested "but very willingly given." Sutton later received a call from Ruckelshaus, according to the spokesman, who quoted Ruckelshaus as saying, "This is nothing personal. I just want people of my own."