The Senate passed a $16.2 billion supplemental appropriations bill last night after making cuts to bring it back under the budget ceiling and rejecting efforts to slash funds for the controversial Tennessee-Tombigvee Waterway, disaster relief to victims of Mount St. Helens and aid to Nicaragua.

The bill, which passed 53 to 22, goes to conference Monday with the House, which passed a $16.1 billion supplemental appropriation for the final three months of this fiscal year.

The key vote yesterday came on an amendment that cut $286.5 million from the total spending package to bring it back in line with the spending ceiling for fiscal 1980 that the Senate adopted two weeks ago.

The cuts were necessary because the Senate had broken the ceiling Friday night by restoring $572.1 million in revenue-sharing funds at the request of Sen. Lowell P. Weicker Jr. (R-Conn.). As part of yesterday's compromise, the Senate agreed to cut $150 million from the Defense Department, mostly for pay; $40 million from Amtrak; $30 million from the Corps of Engineers, and $71.5 million of the revenue-sharing package.

Sen. Warren G. Magnuson (D-Wash.), chairman of the Appropriations Committee, and Sen. Ernest F. Hollings (D-S.C.), chairman of the Budget Committee, said the cuts were necessary to show that the Senate is serious about restraining federal spending and following the budget process.

Sen. Robert C. Byrd (D-W.Va.), the majority leader, told reporters yesterday that Republicans who followed Weicker's lead in busting the budget ceiling Friday night were speaking with "forked tongues" by preaching fiscal restraint on the one hand and voting to pierce the budget ceiling on the other.

Magnuson told concerned senators that the Pentagon could easily absorb the $150 million cut -- part of $7 billion in the bill for defense. "They spill that much in a week over there," he said.

The liveliest debate of the day came in mid-afternoon when Sen. John H. Chafee (R-R.I.) offered an amendment to cut $58 million for continued work on the Tennessee-Tombigbee Waterway. The project would create a 450-mile canal from Tennessee to the Gulf of Mexico and is estimated to cost $3 billion.

Critics, such as Sen. Daniel P. Moynihan (D-N.Y.), have described the project as "cloning the Mississippi River." Chafee said that the project could be likened to America's experience in Vietnam and suggested that Congress cut its losses now.

Proponents of the waterway quickly countered that it was necessary for transporting coal for an energy-hungry nation. Senators from the region, ranging from John C. Stennis (D-Miss.) to Howard H. Baker Jr. (R-Tenn.) to Howell Heflin (D-Ala.), have lined up to speak in praise of the project.

Baker and Heflin ignored Chafee's inference about cutting losses and said it was necessary to complete the project because more than $800 million has already been spent.

"What would the papers say?" 'That's the Senate's ditch,'" Heflin said. "It would turn out to be a monument to a wrong decision."

As the debate continued into the evening, Sen. Jesse Helms (R-N.C.) began to offer a series of amendments aimed at cutting some of the $952 million the bill earmarked for aid to victims of the Mount St. Helens disaster. That total is $118 million more than the House bill appropriated and is largely attributed to Magnuson's efforts.

Helms said he wasn't quarreling with the need for disaster aid, only with the process for appropriating long-term recovery loans without proper hearings.

Magnuson, Sen. Henry M. Jackson (D-Wash.) and several others attacked the Helms suggestion and easily won, on a 55-to-24 vote, a motion to table the measure. A similar Helms amendment was tabled, 77 to 6, before he withdrew his remaining proposed cuts.

In a final effort, Helms tried to cut $75 million in aid to Nicaragua from the bill. He said the money shouldn't be spent on what he termed the "Marxist government" that rules the Central American country. But Sen. Frank Church (D-Idaho), chairman of the Foreign Relations Committee, and others argued that it is worth the gamble to aid the Sandinista rebels who overthrew Anastasio Somoza a year ago. Backers of the aid provision won a motion to table Helms amendment, 44 to 33.