The D.C. City Council approved a negotiated agreement last night that will give city firefighters a one-time 3 percent salary bonus this year and raises of 4 percent, 4 percent and 1 1/2 percent for the next three years.

The cost of the agreement, reached by representatives for Mayor Marion Barry and the International Association of Firefighters, Local 36, is $5.06 million in salary increases and $3.9 million in fringe benefits over the life of the contract. The 1,265 firefighters are to receive the bonus later this month.

In other action, the City Council gave initial approval to:

* Legislation authorizing the issuance of up to $70 million in revenue bonds to finance rehabilitation of Georgetown University facilities. As part of the loan, the university must agree not to discriminate against any groups. The condition was added after local gay organizations complained that the university had failed to recognize the activities of homosexual student groups.

* An amendment that would give Barry authority to set rates for contracted hospital care for indigents. The council sets rates now. The city budgeted $4 million for medical charities for fiscal 1985 and 1986.

* A bill that would prohibit state revenue officers from conducting surveillance operations outside District liquor stores. Maryland and Virginia limit the amounts of liquor that can be brought into their jurisdictions and had been granted permission to station agents near District stores. The City Council says the presence of agents has caused disturbances and hurt sales.

Council member H. R. Crawford (D-Ward 7) also introduced a bill that would exempt police officers below the rank of lieutenant from the District's residency requirement. Under the 1980 law, officers hired recently must live in the District; 36 officers and firefighters recently were given 10 days to prove they live in the District or face dismissal.