The price of a dormitory room at Bowie State University, an issue that triggered the campus's biggest student protest in two decades, will rise by 3 percent in the fall under fees set yesterday by the University of Maryland Board of Regents.

The increase complies with terms of a bargain negotiated in April between campus administrators and students, who took over the administration building and virtually shut down classes to protest proposed increases in various school fees.

Students began their 30-hour protest after learning that the university was planning to increase dormitory fees by 20 percent for the coming year, while raising dining hall prices by 4.5 percent and a required athletic fee by 41 percent.

The takeover ended when Bowie's president, James E. Lyons, agreed to smaller increases in exchange for a $15 increase in a student campus construction fee that the school had not planned to change.

In Maryland, such price changes must be approved by the regents, the board that governs 11 state-supported colleges and universities.

Under the 1990-91 fees adopted by the regents yesterday, Bowie students will pay $1,730 for a typical dormitory room. A full meal plan will cost $1,540, a 1.6 percent increase, and the athletic fee will be $185, a 2.8 percent increase. With tuition and other fees, the cost of attending Bowie next year will be $5,457 for Maryland undergraduates, the lowest in the state.

The regents also set fees for the state's other public college and university campuses, with increases in tuition, room and board ranging from 4.6 percent to nearly 9 percent.

At the University of Maryland at College Park, the state's largest campus, tuition, required fees, a room and meals will be $6,977 for Maryland undergraduates. The 8.6 percent increase will make College Park the most expensive public university for state residents.

Next to Bowie, the least expensive school will be the University of Maryland Eastern Shore, a small, historically black campus in Princess Anne, where the total price for Maryland undergraduates will be $5,618. In general, the prices at Maryland schools will be somewhat lower than those in Virginia, where Gov. L. Douglas Wilder persuaded the General Assembly this spring to set a limit on tuition increases. The ceiling restricts the increases for Virginia undergraduates to 6.5 percent for four-year colleges and universities and 7.5 percent for two-year community colleges.

The assembly gave Wilder the authority to withhold state aid from schools that exceed the limit. So far, the effect has been most pronounced at Virginia's community colleges, which had planned to raise tuition by 11.5 percent, the first increase in five years, but complied with the limit instead.