Like a schoolboy accepting a spoonful of some particularly vile medicine, the House of Representatives yesterday finally swallowed the waterway toll bill and sent the measure on to further skirmishes in the Senate.

By a deceptively lopsided vote of 331 to 70, the House approved legislation to require commercial barge lines to pay for their use of federally built and maintained inland waterways.

It was the first time the House has ever voted any form of waterway charge. But the bill was still a disappointment for supporters of the waterway toll, because the House versior is considerably weaker than S. 790, the waterway bill that the Senate passed in June.

The bill passed yesterday would impose a fuel tax of 6 cents a gallon on the diesel fuel that drives the barges. That would bring in less than 10 percent of the government's annual expenditure on inland waterways. The Senate bill, in contrast, would impose a system of fees rather than a tax and would recover all of the federal money spent on maintenance of waterways, and 50 per cent of new construction costs as well.

Even the relatively mild House version was a blow to the barge industry, which has never paid a cent for its use of the nation's 25,000-mile inland waterway freight network.

But the barge owners were forced to back the bill because it had been linked to authorizing legislaion for Locks and Dam 26, a $432 million barge facility on the Mississippi at Alton, Ill. The Alton authorization was approved yesterday as part of the toll legislation.

The House bill, in short, was a compromise - one that left hardly anyboyd really happy, but hardly anybody unhappy enough to vote "no." Accordingly, the two hours of debate yesterday turned into one chorus of complaints.

Several members - including Berkeley W. Bedell (D-Iowa), and Joe Skubitz (R-Kan.) - said the waterway tax would be too low. Just as many - including Otis G. Pike (D-N.Y.) and M. G. (Gene) Snyder (R-Ky.) - said just as angrily that it would be too high.

Pike shouted that the fuel tax was a "shotgun bill," which would pass only because the Alton project was being held hosttage. Rep. William M. Ketchum (R-Calif.) disagreed with Pike about the wisdom of the legislation, but agreed with him on the procedure. "We shouldn't be operating under a blackmail principle," Ketchum intoned unhappily.

Those who supported the bill could reply only that it was necessary medicine, however distasteful. "If we don't use the shotgun, we'll be aiming a cannon at the most vital arm of our transit system," observed Rep. Bill Frenzel (R-Minn.)

House passage reflected once again that the waterway bill, which was considered almost hopeless when it was introduced last winter, has had something of a charmed life.

When the bill arrived at the House after the Sneate vote in June, it seemed doomed when House members raised a consitutional challenge: the waterway toll would raise revenues, and the Consitution mandates that revenue bills must originate in the House.

House Speaker Thomas P. O'Neill Jr. (D-Mass.) stepped in then to save the bill from constitutional extinction by developing in the compromise fuel tax plan that finally passed yesterday.

The waterway user fee has prompted a furious lobbying campaign, pitting railroads, enviromentalists, and the Carter administration, which support the fee, against barge lines and farm groups, which oppose it.

Yesterday, though, few lobbyists were evident. Everyone considered the House vote a foregone conclusion. The real battle would take place, once again, in the Senate, which must now reconsider the waterway toll in the light of the House action.