Interior Secretary William P. Clark yesterday reorganized his department, replacing three top aides to former secretary James G. Watt and signaling plans to put his own stamp on controversial mineral-leasing programs that brought Watt under fire.

In the department's No. 2 job, Clark replaced J.J. Simmons III with Assistant Treasury Secretary Ann Dore McLaughlin, public affairs chief of the Environmental Protection Agency in the Nixon administration, under William D. Ruckelshaus and Russell Train.

Simmons, one of the administration's highest-ranking blacks, is to be nominated to a seat on the Interstate Commerce Commission.

Clark also replaced Acting Assistant Secretary William P. Pendley and his assistant, Dave Russell, two key architects of Watt's programs for accelerating development of offshore oil and gas reserves and western coal.

Pendley's duties, which included managing offshore oil leasing and most mining permits, will be divided between Assistant Secretaries Garrey E. Carruthers and Robert N. Broadbent, Watt appointees named to head two new divisions of the department created in the reshuffling.

In place of Russell, a former Republican congressional aide with ties to the conservative Heritage Foundation, Clark named named William D. Bettenberg, a longtime Interior Department civil servant. Bettenberg becomes head of the Minerals Management Service, which oversees offshore oil and gas leasing and royalty collection.

The changes come in a week during which Clark made several policy decisions that appeared to depart from his predecessor's approach. In one, he had withheld a planned announcement by Pendley and Russell of major forthcoming sales of offshore leases, citing concerns about negative environmental and other impacts.

Clark frustrated many members of Congress during his confirmation hearings and his first weeks in office by declining to say whether he planned to reverse Watt's major policies or replace his aides. Yesterday's changes were interpreted by several officials as signals of a shift in style but not necessarily substance.

Carruthers, who will now direct all mineral-leasing and land-conservation programs, directed Watt's controversial coal-leasing program, which is being investigated by a congressionally authorized commis- sion because of charges that the program amounted to a "giveaway" of public coal reserves.

Congressional investigators put much of the blame for alleged mismanagement of the program on Pendley and Russell, but Carruthers was its chief defender during congressional hearings earlier this year.

Broadbent, an active Nevada Republican, was commissioner of reclamation under Watt, keeping a low profile while heading programs on water resource development and irrigation.

Other key political appointees closely linked to Watt's policies were not moved. They include Solicitor William H. Coldiron; Assistant Secretary G. Ray Arnett, who headed fish, wildlife and parks programs; Bureau of Land Management Director Robert F. Burford, and press secretary Douglas Baldwin.

J. Steven Griles, who helped carry out Watt's controversial changes in strip-mining regulation, will serve as Carruthers' assistant.

Clark said the reorganization and job shifts aim to "emphasize the administration's concerns for advancement of natural resources science and research, water resources management and protection and preservation of the nation's lands."

McLaughlin, in her first assignment as undersecretary, is to review the Interior Department's relations with the media and Congress, a constant battleground during Watt's tenure. Officials said they expect her to recommend several major changes in the department's offices dealing with both.

Republican and Democratic members of Congress voted earlier this year to place a moratorium on Watt's coal-leasing program and curtail several initiatives involving oil leasing, offshore resources and wildlife refuges. Democrats in Congress and conservationists accused Watt of silencing his employes and impeding public access to Interior Department documents.

After her appointment was announced, McLaughlin praised Clark's "commitment to open communication with Congress, environmental and resource groups, the press and the public." She said she has had a longtime interest in environmental and natural resource issues.

McLaughlin, who directs public affairs for the Treasury Department, was president and founder of a public relations firm before joining the Reagan administration.

Interior Department sources said Clark views the changes as neither a departure from nor a continuation of Watt's agenda but as part of a review, requested by President Reagan, of policy, personnel and process at the department.

Under Watt, there was a marked shift toward promoting development of natural resources and curtailing conservation programs. He imposed a near-moratorium on purchasing new land for national parks and wildlife refuges, initiated an eight-fold increase in the amount of public coal reserves leased to private companies and began a program to offer the entire U.S. coastline for offshore oil and gas leasing by 1987.

Jay D. Hair, executive vice president of the 4 million-member National Wildlife Federation and one of Watt's most vocal critics, said that he does not consider yesterday's changes adequate and hopes that Clark will announce more.

"We want more than a cosmetic reorganization. We hope to see substantive changes in personnel and policy. It's the people he puts in the jobs, not where they are on an organizational chart, that matters," Hair said.

In the reshuffling, Clark combined all Interior Department programs dealing with water, geology and scientific research under Broadbent, the new assistant secretary for water and science.

Carruthers' new division will oversee strip-mining regulation, the Minerals Management Service and the 350 million acres of federal land in the Bureau of Land Management, which includes conservation planning and programs involving mineral leasing, grazing and recreation.

Pendley and Russell were not assigned to new posts in the reorganized department, but officials said they will remain as "consultants" until they finish current projects.

Others appointed to new posts include Harold W. Furman II, now an assistant to Carruthers, who was named Broadbent's deputy; Laura Dietrich, a State Department official, as special assistant to Clark in charge of personnel and intergovernmental relations; and Joseph W. Gorrell, a long- time Interior Department budget official, who replaces Bettenberg as deputy assistant secretary in charge of policy and budget review.

Last week, Clark wrote a letter to David F. Linowes, chairman of the commission investigating Watt's coal-leasing program, declining Linowes' offer to allow several departmental employes to comment on drafts of the panel's report.

The letter was sent after it was learned that several of Watt's aides had secretly supplied the commission with rebuttals to testimony critical of the program.