Congress yesterday sent President Reagan its first three appropriations bills for next year while the Republican-controlled Senate, defying veto threats, refused to cut spending for food stamps and other nutrition programs in a fourth bill.

By lopsided votes, both houses approved funding of $55.8 billion for the Department of Housing and Urban Development and 17 independent agencies, $14.3 billion for energy and water programs, and $1.5 billion for legislative activities.

Congressional leaders said the president is expected to sign all three bills, although the HUD measure exceeds the administration's request by $6.2 billion, mostly for subsidized housing.

The HUD bill also includes $295 million more than Reagan originally requested for the troubled Environmental Protection Agency. But the $4 billion allocation, including $1.1 billion for EPA operations and $410 million for the toxic-waste Superfund, is in line with a recent request from William D. Ruckelshaus, the new EPA administrator.

The bills' smooth passage appeared to be the calm before the storm. With Reagan vowing to veto spending bills that he regards as "budget-busters," Congress is bracing for a veto confrontation that could begin with an agriculture spending bill that the Senate approved yesterday by a vote of 77 to 18.

The administration has labeled both House and Senate versions of the measure as "unacceptable," charging that its anticipated funding levels for farm and nutrition programs would lead to "enormous additions to the deficit" even though it is technically $67.4 million less than Reagan proposed.

Warning that the measure is a "prime candidate for a veto," Senate Agriculture Committee Chairman Jesse Helms (R-N.C.) tried unsuccessfully to delete provisions that he said would force an estimated $1.3 billion in supplemental appropriations next summer for food stamp, child nutrition and women's and infants' feeding programs.

Like the House, the Senate Appropriations Committee had accepted Reagan's scaled-back spending levels for these programs but made them apply for less than a full year, meaning Congress will have to provide more money for them if, as expected, it refuses to go along with program cuts recommended by Reagan.

"We should stop playing games with federal spending," said Helms, claiming that his effort had Reagan's support.

But Sen. Thomas F. Eagleton (D-Mo.), chairman of the Agriculture appropriations subcommittee, contended that Helms' proposal could lead to across-the-board cuts in benefits. And Sen. Robert J. Dole (R-Kan.), chairman of the nutrition subcommittee, contended that "we've gone about as far as we can go" in cutting such programs.

Helms' proposal was defeated, 73 to 24.

Not only did the Senate not cut its Appropriations Committee's draft of the measure, it also added about $200 million, including $96 million for the Food for Peace program.

Senate Budget Committee Chairman Pete V. Domenici (R-N.M.) said estimated spending levels in the bill, projected for a full year, would exceed Reagan's request by $1.5 billion and the recently approved congressional budget by $385 million. Senate Majority Leader Howard H. Baker Jr. (R-Tenn.) said he would oppose the measure if it wasn't reduced in conference with the House.

In the House, the energy-water bill generated the sharpest controversy, especially from Rep. Silvio O. Conte (R-Mass.) who complained about inclusion, at Senate insistence, of $22.3 million for the Garrison irrigation project in North Dakota. Conte, who has fought the project for years as an expensive "boondoggle," said yesterday, "I can't fight the odds any longer. This is my last battle on this one."

Controversy over proposed use of an old reactor at the Savannah River plutonium processing plant was resolved in conference by a requirement for completion of an environmental impact statement by next January as a condition for restarting the reactor.

The legislative appropriations bill was approved without a Senate-passed provision calling for a consulting architect to supervise restoration of the Capitol's crumbling West Front. Sen. Alfonse M. D'Amato (R-N.Y.), who made the proposal in light of Capitol Architect George White's long-held preference for an extension instead of restoration, agreed that the provision would fit better in a supplemental appropriations bill that already contains funds for restoration work.