The House yesterday, passed 361 to 43, a bill authorizing $17 billion over three years to clean up the nation's waterways and changing procedures to try to speed up the lagging program.

The bill is intended as a vehicle to free President Carter's $4 billion local public works jobs bill, which has been held hostage for four weeks in a House-Senate fight over water pollution policy.

But unless conferees can reach agreement on these issues today, the bill to create 160,000 construction jobs will be delayed for at least 11 more days by the Easter recess which the House begins tonight.

The water pollution fight pits congressmen who want to speed up the sewage treatment program against environmentalists who fear they are cutting corners in their rush.

Five years ago Congress authorized $18 billion for a three-year program to help local governments build treatment plants. But only two-thirds of the funds have been committed and only 10 per cent actually spent on completed projects, according to the House Public Works Committee. Majority Leader Jim Wright (D-Tex.) said he knows of no other program that has been "more disappointing" to its sponsors.

Last year the House passed a bill aimed at cutting red tape and speeding up machinery for giving the money away. It died in a conference with the Senate.

Last month, after the House had passed the President's public works bill - the heart of his program to stimulate the economy - the Senate added $9 billion to extend the water pollution funding two more years. But it included none of the amendments the House wanted.

House managers feared that if they let the grant money go they would lose all leverage for legislation to reform the water pollution program. So they refused to go to conference with the Senate and concentrated instead on drafting the water pollution bill as a bargaining tool. A conference cannot agree to anything that did not appear in one of the two versions.

The heart of the House speedup would allow the states to take over the Environmental Protection Agency's function of approving grants to local governments subject to EPA takeover if the states don't perform adequately. Environmental groups don't trust the states to demand sufficiently strict standards.

Another charge would reduce from three to two the separate application steps necessary to a project costing less than $1 million. This would save up to one year in processing time, backers said.

The House bill would extend, case by case, the July 1 deadline for all local governments to be operating secondary facilities that remove solids from sewage. About half the nation's cities can't meet the deadline and would be in violation of the law unless it is changed.

The bill would also permit cities to finance operating costs of sewage treatment plants out of property taxes rather than the currently required use fees.

The most controversial provision in the House bill - one that opponents failed to change on a voice vote yesterday - would restrict the power of the Army Corps of Engineers to regulate dredging and filling of the nation's waterways.

A 1975 federal court decision construed the 1972 Water Pollution Control Act as giving the engineers control over not just navigable waters but all the waters. Farmers feared they would have to obtain a permit to widen a ditch or enlarge a stock pond.

The House bill restrict the engineers' authority to navigable waterways and adjoining wetlands; environmental groups fear this will endanger most of the excluded wetlands where fish and wildlife breed. An attempt by James Cleveland (R-NH) to exempt farm and ranch operations from regulation but otherwise to retain the broad scope of the engineers' authority was rejected, as it was last year.

The bill also contains $15 million to help build a new jail in Boston. House Speaker Thomas P. O'Neill (D-Mass.) explained that Boston and Massachusetts are to swap land on which the city will build the jail and the state a sewage treatment plant. The federal aid to the city represents money that would otherwise have to be spent filling land for the plant site, O'Neill said.