The Reagan administration's deregulators are getting ready to take on a much-maligned and often disobeyed law requiring boats not to discharge untreated sewage into the nation's waters.

The Environmental Protection Agency and the Coast Guard, which share responsibilities for monitoring and enforcing the Clean Water Act program, announced last week that they are seeking comments on how the program should be modified. In a posting in the Federal Register, the agencies said they were reviewing it "because of the many complaints by the public regarding the costs and impracticability of the existing program."

Changes in the program, which went into effect two years ago, might require legislative changes, an EPA official said. The law requires boats with installed heads to have either "flow-through" devices to treat the sewage before it is discharged or holding tanks that can be pumped out later at onshore facilities. The flow-through devices range in price from $200 to $400 and the holding tanks between $100 and $300.

The law also allows states, with EPA's approval, to designate areas where boats can be barred from discharging. Virginia has a request pending before EPA to give that designation to the lower Rappahannock River.

Pressure had been growing even before President Reagan took office to change the rules, which the Coast Guard estimates are disobeyed by at least 75 percent of recreational boat owners. At the behest of Sen. Charles McC. Mathias (R-Md.), then a member of the Senate Appropriations Committee, the panel last year asked EPA to study the program and alternatives.

In the meantime, the Coast Guard has had its budget cut and its priorities directed elsewhere, to areas such as drug enforcement and immigration violations.

These rules are "really small potatoes" that have an impact on the ordinary person, said Steven Schatzow, deputy assistant administrator of EPA for water regulations and standards.

"They are nuisance regs," said Mike Scuilla of the Boat Owners Association of the United States. "There was no scientific basis for them."

But the boat owners group is concerned that rather than waiving the requirements for recreational boats, the administration will turn over all regulation to the states. If a boat owner had to contend with the regulations of many different states --such as in an area like the Chesapeake Bay--it would lead to chaos, group officials said.

EPA and the Coast Guard are accepting comments on the program through Feb. 22.