President Reagan vetoed legislation yesterday designed to end a long-running dispute over water rights between an Arizona Indian tribe on one side and mine owners, farmers, cattlemen and municipalities and much of the rest of the state's political establishment on the other.

The legislation, in effect a congressional effort to settle out of court a lawsuit brought on behalf of the Papago Indian tribe, would have committed the federal government to paying several million dollars to the Papagos to resolve the dispute.

Reagan, using his veto power for only the fourth time, called the bill "a multi-million dollar bailout of local public and commercial interests at the expense of federal taxpayers throughout the nation.

"It is a prime example of serious misuse of federal funds. It asks the federal government to pay the settlement share of the mining companies and other local water users whose share should more properly be borne by the defendants themselves."

Rep. Morris K. Udall (D-Ariz.), whose staff helped mediate the dispute and who introduced the "Southern Arizona Water Rights Act" in the House, had hoped to resolve the Papago's claims so that they would not interfere with development of the Central Arizona Project, a massive multibillion-dollar water-diversion pipeline scheduled to deliver Colorado River water to the booming Phoenix and Tucson areas.

Udall, declaring himself "angered" by the veto, threatened to seek an override.

It was the federal government, acting as trustee for the 16,000-member Papago tribe, who filed suit in 1975 against 1,700 big water users. The suit argued that off-reservation pumping adjacent to one of the tribe's reservations had caused wells to dry up and the Papago's economy to wither. The tribe sued for damages for past injuries and asked the court to enjoin the big water users from further infringing on their water rights.

Fearing that the litigation could drag on for years and be a stumbling block to the Central Arizona Project, Udall's staff brought together the wide assortment of interests in an effort to mediate the dispute. Their agreement guaranteed the Papagos a water supply. It established a $15 million trust fund for an extension of reservation irrigation systems, promised a share of water from the Central Arizona Project and additional treated effluent from the Tucson sewage treatment plant.