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The National Marine Fisheries Service today released new guidelines for water operations on the Sacramento-San Joaquin River Delta to protect salmon, killer whales and other fish, a step that state officials say could reduce overall water exports as much as 10 percent each year.

The decision further tightens the spigot from one of San Diego’s major water sources and expands the roster of endangered species that must be protected when the state pumps water out of the delta.

It also means the Sacramento Delta’s problems are no longer solely about the delta smelt, the endangered three-inch fish whose population has plummeted in recent years. The delta smelt became the poster child for the decline of the delta’s ecosystem. The new guidelines add protections for two runs of Chinook salmon, as well as the Central Valley steelhead, green sturgeon and the killer whale population from Puget Sound, which ranges south to feed on salmon that migrate through the delta and into the Pacific.

The population of Chinook salmon (also called king salmon) that’s found in the delta plummeted to historic lows last year, prompting an unprecedented closure of commercial salmon fishing from the U.S.-Mexico border to Oregon.

In its guidelines released today, the federal fisheries service concluded that the delta’s two major water pumping operations — the State Water Project (which supplies San Diego and other cities) and the Central Valley Project (which primarily supplies farms) — had created “an altered environment” that is negatively impacting the salmon and other species.

“What is at stake here is not just the survival of species but the health of entire ecosystems and the economies that depend on them,” said Rod McInnis, southwest regional director for the fisheries service, in a news release.

The service said fish were affected by unnaturally warm water temperatures that occur when cold snowmelt is trapped in reservoirs; by the massive pumps that pull water out of the delta; and by flood-control operations that reduce available habitat.

The fisheries service said the restrictions would reduce average exports from the State Water Project by about enough to supply 400,000 households annually. Those impacts won’t occur immediately, the service said.

The restrictions won’t change the 8 percent supply cut that the San Diego County Water Authority, the local supplier, will begin delivering to local cities starting July 1. Dennis Cushman, the authority’s general manager, said impacts won’t likely be felt until 2010 but could manifest later this year.

“We were expecting bad news, and we got what we were expecting,” Cushman said. “It’s another shot across the bow of Southern California’s water supply reliability.”

ROB DAVIS

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