Federal directive to cut California water delivery

Warning that salmon and other fish species are in danger of extinction, a federal agency Thursday issued directives that will guide the way dams, pumps, canals and other waterworks in California operate to help ease pressure on the Pacific coast’s collapsing salmon fishery.

The biological opinion from the National Marine Fisheries Service affects waterways from the American River to the San Joaquin and will reduce water deliveries to farmers and urban users by about 5% to 7% annually, according to officials. Complying with the court-ordered prescriptions could cost “hundreds of millions” and would be passed on to water users, according to a federal water manager.

The 800-page document is the latest in a series of actions to address the increasing obstacles to the salmon’s twice-yearly runs: upstream migration for spawning, when the fish require cool, abundant water, and downstream emergence of juveniles, which must negotiate the San Joaquin-Sacramento River Delta’s maze of gates, canals and diversions to reach the sea.

Maria Rea, the federal Fisheries Service officer primarily responsible for the biological opinion, said as much as 98% to 99% of young fish attempt- ing to exit the San Joaquin water system are succumbing to pollutants, unfamiliar food, predators and pumps removing water for irrigation and urban use.

The new document replaces a 2004 biological opinion that found that increased pumping of water to the Central Valley and Southern California posed no harm to threatened and endangered populations of California salmon, steelhead and green sturgeon. A federal judge last year ruled that the agency had erred and ordered it to redraft the opinion.

Rea called the document “One of the most complex and scientifically challenging” the agency has ever undertaken, and said, “What is at stake here is not just the survival of the species but the entire ecosystem that depends on them.”

Some commercial fishermen applauded the changes. This is the second straight year that the state’s salmon fleet has been barred from fishing off the coast. California officials estimated that the ban equates to a loss of 2,200 jobs and $250 million in revenue.

“We’ve given as much blood as we can give,” said Larry Collins, vice president of the Pacific Coast Federation of Fishermen’s Assns. .

The announcement was not universally embraced, though. “Public water agencies have faced cutback after cutback in failed attempts to boost fish populations,” said Laura King Moon, assistant general manager of the State Water Contractors.

Don Glaser, regional director of the Bureau of Reclamation, the federal government’s water management agency, said his office would “provisionally” accept the directives but hasn’t had a chance to fully assess the implications.

Taken with federal requirements to reduce pumping to protect the delta smelt, Thursday’s announcement will stress California’s water system, Glaser said.

“I believe you are going to see less reliable water, particularly as it relates to farming activities in the Central Valley,” he said, “and it will become more difficult to find replacement water for the urban growth that is anticipated in Southern California.”

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julie.cart@latimes.com