In the long war between whites and Indians over commercial fishing rights in salmon-rich Puget Sound, the fish and the biological order that supports them have wound up the losers.

When the U.S. Supreme Court this summer upheld a five-year-old federal court decision that reserved for the Indians up to 50 percent of the allowable salmon catch, the salmon fishery was suffering from international conflict, alleged mismanagement, a surplus of commercial fishermen and environmental pressure. While more than 7 million salmon will be taken from Puget Sound and adjacent Washington state coastal waters this year, biologists, boatmen and Indians have warned that important stocks of wild salmon are endangered.

The complexities and competing interests of an industry in which about 30 federal, Canadian, regional, state and Indian entities share jurisdiction were demonstrated anew today when the U.S. State Dept. announced a ban on the importation of Canadian tuna. The ban was ordered in response to the seizure by Canadian patrol boats of American boats that were fishing for tuna in British Columbia waters two weeks ago. The Canadian action was taken in apparent retaliation for a U.S. prohibition against Canadian roe hearring fishing in American waters.

Though not directly related to the salmon controversy, the seizures reflected the growing pressures on an industry that is an important source of food and revenue on both sides of the boarder. For the past two years a "cold war" has existed between the U.S. and Canadian governments over the salmon fishery, most of it centering on the proper division of fish schools that migrate up Puget Sound and into the Fraser River, the principal river of British Columbia.

From 1970 to 1978, the two nations allowed the fishermen of one country to fish for salmon off the coasts of the other. Prolonged negotiations for renewal and modification of the agreement have so far proved fruitless.

In addition to the international conflict and the domestic battle between whites and Indians, various groups of commercial fisherman are fighting each other for preference in the allocation of fishing grounds, U.S. Attorney James Waldo, who negotiated on behalf of a federal task force that proposed a settlement in the salmon and steelhead fisheries, recalled that the solution of most fishermen was to limit the catch of someone else.

"I became convinced that the problem was going to have to be solved on the water, by mutual agreements, rather than in court," Waldo said, "It really isn't a legal battle as much as an economic and social one."

While Waldo worked on the settlement he became aware of the huge pressure that the salmon were under from overfishing.

"What brought it home to me were the statistics from one day in 1976, when 750,000 salmon were caught by Americans and Canadians in the Fraser River," Waldo said. "It's obvious that no fishery could long withstand that kind of pressure."

In order to preserve the fishery, Washington state has shortened salmon seasons for most commercial fishermen. The action, in turn, has created further factionalism and led to bitter new accusations against fisheries' officials in Olympia, the state capital.

Protesting a recent 10-day closure, troll fishermen recently took out advertisements in Seattle newspapers, in the form of an open letter to Gov. Dixy Lee Ray. The fishermen claimed they were "systematically being forced out of the fish industry" by the Washington State Department of Fisheries.

However, it is the Indians' long and finally successful fight for vindication of treaty rights reaching back to the 1850s that has attracted most national attention. But the Indians, despite the widely publicized federal court decision allowing them up to 50 percent of the salmon catch, have never taken even half of their entitlement.

Few of the Indians have boats, and many of the salmon the Indians theoretically were entitled to were caught by others before they migrated to tribal waters. The situation is reversed in the case of the smaller steelhead trout, for which Indians fish first at the mouths of rivers and catch the greatest share.

Whatever the Indian catch, Indians have been blamed by most white fishermen for most of the problems besetting the commercial salmon industry. From the time that U.S. District Court Judge George Boldt ruled in favor of the Indians in the treaty rights case on Feb. 12, 1974, to a 6 to 3 U.S. Supreme Court decision on July 2, 1979, which in the main upheld Boldt's ruling, Indians were a target for abuse and criticism. Incidents including fights and a few shootings, became commonplace on Puget Sound and its tributaries.

In actions the Supreme Court majority compared to Southern resistance to desegregation, Washington state legal officials refused to enforce Boldt's order. They instead denounced the judge, and encouraged fishermen to believe his decision upholding treaty rights was capricious and unlikely to stand up on appeal. Reluctantly, the federal government took over management of the salmon fisher.

The Supreme Court restored the fishery to the state, with a warning that federal officials would step in again if Boldt's order wasn't enforced. At the same time, the court also softened the potential impact of Boldt's decision by ruling that any fish caught for ceremonial or subsistence purposes will have to count against the Indians' 50 percent share.

Indians acclaim the Supreme Court decision, but some of their leaders fear that Washington state will once more fail to enforce the law.

"If the state manages the fishery, it's doomed," says Nesqually tribal recepresentative Billy Frank Jr. "The racism which led to the state's resistance is still there and the unwillingness to enforce the treaties is still there."

Frank is a member of the Northwest Indian Fisheries Commission, an organization of 19 tribes which has tried to coordinate fishery management in the region.

But there are signs of a new attitude in Washington state which focuses on improvement of the fishery rather than on criticism of the Indians or the federal courts.

"It's not the Indian fisherman who have caused supplies of once plentiful fish to vanish," editorialized the Seattle Post-Intelligencer after the Supreme Court ruling. "It's pollution, poor logging practices, thoughtless placement of dams and a sprawling population. What's needed are ecologically sound conservation and management practices."

Paul Anderson, executive manager of the Puget Sound Purse Seine Vessels Assocation, said that fishermen in his group recognized that "we have to live with the outcome and improve the fishery," Like many industry officials, Anderson is counting on a proposed $90 million federal program aimed at building salmon runs and providing funds to buy up and retire the licenses of non-Indian fishermen.

The sum is far less than the $208 million recommended by an interagency federal task force, but many fishermen think Congress will appropriate more money through the influence of Sen. Warren G. Magnuson (D-Wash.).

Anderson said that if the present fleet of 4,000 commercial boats on the sound is pared to 2,000 over the next decade, the remaining fishermen could make a living. Seven of the 10 top purse seiners have said they will sell out if funds are available.

Another serious problem, say some biologists, is a reduction of wild stocks of salmon because of mismanagement at hatcheries. In one case, hatchery salmon were delivered to the mouth of a river only to be promptly devoured by young wild fish making their way to sea. In other cases, crowded conditions in hatchery pools have caused disease that has been transmitted to wild fish.