Boston will receive next year more than $100 million from the federal government to begin cleaning the Boston harbor, which many environmentalists consider to be one of the nation's most polluted bays.

Congress allotted the money to the city as part of the National Clean Water Act, which passed over President Reagan's two-time veto last week. The money will be distributed next October and is portion of $2.4 billion slated for water clean-up throughout the country.

In addition to giving Boston $100 million, Congress will give nearly $620 million to the Commonwealth of Massachusetts, part of which will be allocated to Boston through special grants.

Massachusetts Water Resource Authority (MWRA) Chief Spokesman Paul Di Natale viewed the passage of the Clean Water Act as a welcome change. "Previous Republican administrations have sponsored environment protection. Unfortunately Reagan's didn't. It's sad [Congress] had to override him, but we're glad we're getting the money," he said. The Senate vote was 86--14 in favor of the act.

City Budget Director and member of the MWRA Robert Ciolek said the passage of the act represents a positive sign for Boston Taxpayers. "There are significantly more federal dollars here. Now we don't have to use as many rate payer dollars. It's important that we can ameliorate the impact of the clean-up on the rate payer," he said.

After the 1972 Clean Water Act expired in 1985, efforts began to pass a second, said Ciolek, who worked with the Mayor's office to lobby for the act. But Reagan opposed the power and authority in spending the act would give federal agencies. Last year, he vetoed the act by allowing it to die without his signature, and he formally vetoed it again last month.

Boston officials said that they were glad the act finally passed. "In terms of large cities' harbors, it's between us and L.A. to say which is the dirtiest," Ciolek said. Federal funds will pay for about four percent of the clean-up, which will cost $2.5 billion, he said.

Not only is sewage that is only halfway purified purposely poured into the Harbor, but, during rainstorms, poisonous sewage accidentally runs into the water, a phenomenon known as combined sewage overflow. This, in addition to the toxicants that over 6,000 industries dump into the Harbor and its tributaries each year, has tainted the water and damaged the Harbor's sea life.

According to Di Natale, the toxicants have polluted over 75 percent of the Harbor's clam flats, and the water's shellfish and groundfish populations have developed fin disorders and malignant tumors.

Ciolek said that although some Boston beaches are open in the summer, it is often unsafe to swim in the Harbor's water, especially after rainstorms.

Part of the federally received funds will be used to construct a tunnel 300 feet below the Harbor through which sewage can be channeled to Deer Island, where a new plant will remove 90 percent of the impurities from the water. Presently, most sewage goes to Nut Island where only 50 percent of the impurities are removed, Di Natale said.

Di Natale added that the MWRA will also construct a pipeline to take the purified sewage two to six miles out to sea. He said the agency will use other funds it receives to construct a system of piers that will transport the over 2,000 construction workers expected to join the clean-up out to the islands.

The Harbor clean-up project will not be completed until 1999.