SAN FRANCISCO — The federal Fish and Wildlife Service this week underscored the imminent threat of extinction facing the delta smelt, a two-inch-long fish native to the Sacramento River delta, when it announced it was considering whether to declare the fish endangered.

California is in a quandary because two-thirds of its residents get water through the pumps that have been killing large numbers of smelt. This year, for the first time, a federal judge’s order kept state and federal water agencies from collecting their usual part of the river water flowing from melting snow from the Sierra Nevada. Water users from the Bay Area to San Diego were affected by the resulting reductions of 20 percent to 30 percent.

This is taking place after a spring that has been one of the driest on record, leaving even less water for the fiercely competitive interests fighting for a share of a dear commodity.

“A comprehensive approach to conserving this fish is going to require onerous restrictions in pumping,” said Timothy Quinn, director of the Association of California Water Agencies.

The distribution of water used to mean “that you killed fish,” Mr. Quinn said, adding, “Now the fish have very strong legal protection, to the point where they are becoming a dominant policy consideration. To protect the fish means losing massive amounts of the water supply.”

A spokesman for the Fish and Wildlife Service in Sacramento, said smelt populations this year were 92 percent smaller than a decade ago. Should the agency decide to change the smelt’s status to endangered from threatened, he said, the protections would be largely the same.

Michael Boccadoro, a spokesman for the Coalition for a Sustainable Delta, a group representing major water users, said that “from an operational perspective,” a status change for the smelt would “make little difference because threatened and endangered species have the same protection.”

Tina Swanson, executive director of the Bay Institute, a conservation organization, said the potential change in the fish’s status “should send up an urgency flag” for regulators that they need to resolve the complex issues involved in maintaining and transporting the state’s water supplies.