The Justice Department has decided to go forward with three school desegregation cases filed in the final days of the Carter administration.

William Bradford Reynolds, head of the department's civil rights division, said yesterday that he has decided to continue suits against school districts in Charleston, S.C.; Lima, Ohio, and Yonkers, N.Y. All three suits charge that schools have intentionally been racially segregated.

Reynolds made it clear in a statement that the department would try to settle the cases without going to trial. " . . . To that end, the attorneys for each of these school districts are being asked to meet in the near future with department lawyers to discuss the possibilities of settlement," he said.

Sen. Strom Thurmond (R-S.C.), chairman of the Senate Judiciary Committee, had written Attorney General William French Smith to ask that the cases be reviewed, and Thurmond brought up the issue again when Reynolds appeared before his committee for confirmation hearings.

"While I don't know all the facts in this case, the Justice Department has indicated that they can work out their problem with the school district, and I'm hopeful they can do so," Thurmond said.

The suit against Charleston, filed Jan. 9, charged that the county's public schools are segregated because of intentionally discriminatory decisions by the state legislature and local school officials.

In the case against Yonkers, a city of 200,000, the Justice Department charged Dec. 1 that the city's public school system and residential areas had intentionally been segregated by a series of school board actions and by placement of public and subsidized housing projects.

In a controversial internal memo last month, Robert D'Agostino, Reynolds' deputy, had angered other lawyers in the division by recommending the Yonkers case be dropped and calling it "the end result of a mind-set in the educational area and one of the opening shots in a new attempt to remake America through coerced residential integration."

Reynolds said yesterday that he is still reviewing the portion of the case that charged Yonkers with violations of the Fair Housing Act.

Justice Department spokesman John Wilson said there have been conflicting court decisions recently involving the Fair Housing Act in Ohio and Manchester. He said the division is studying the implications of those court decisions before deciding whether to go ahead with that part of the Yonkers case.

The case against Lima, a city of 53,000, was filed Dec. 4.

Smith and Reynolds have expressed opposition to busing as a remedy to racial discrimination.