Salmon, steelhead and sturgeon in the Central Valley are being driven to extinction by Delta pumping systems and upstream reservoir operations, according to a draft federal report.

The National Marine Fisheries Service has not yet released the report, but it was discussed at a meeting of scientists in Sacramento on Thursday.

The impacts are so significant that the agency is also studying whether killer whales in the ocean could be imperiled by declining Central Valley salmon, their primary prey.

The grave findings suggest that California's efforts to serve thirsty farms and cities while sustaining healthy fisheries will only get more difficult.

A final version of the report, called a biological opinion, is expected by March 2. The Endangered Species Act empowers the fisheries service to impose new rules on state and federal water systems to protect the fish.

The state and federal governments operate separate reservoir and canal systems that collect Northern California's snowmelt and distribute it to cities, suburbs and farms statewide. These systems have dammed off hundreds of miles of fish habitat and altered the timing and temperature of river flows.

Given the findings, the fisheries service could require the California Department of Water Resources and U.S. Bureau of Reclamation to change reservoir operations, improve river habitat and divert less water from the Sacramento-San Joaquin Delta to Southern California. Hatchery practices might have to be changed to protect wild fish.

The details of these forthcoming rules were not revealed Thursday. Officials at both water agencies have seen the full draft but declined to comment on the specifics.

"To take additional hits (in water supply) will be very problematic for us," said Jerry Johns, deputy director of the state Department of Water Resources. "Our goal is to protect these fish species, and we've got to make sure we do that effectively. But we've got to do it in a reasonable way."

The biological opinion has a long and troubled history.

A version completed in 2004 reached similar findings. But a regional director at the National Marine Fisheries Service, a political appointee, altered the final report to show, instead, that the species would not be imperiled by water operations.

Conservation groups sued, and last year federal district Judge Oliver Wanger ruled the agency's actions were "arbitrary and capricious" and violated the Endangered Species Act. He ordered a new report prepared by March of this year, but allowed water operations to continue unaltered until then.

Under current rules, the state Department of Water Resources and U.S. Bureau of Reclamation coordinate their operations to boost water pumped through the Delta to farms and cities south. One of their tools is to manipulate the timing of water releases from reservoirs, including Shasta, Oroville and Folsom.

Fisheries Service biologists said Thursday that the current system, with its emphasis on water for people, does not provide adequate cold water for spawning habitat in the Sacramento River. This will worsen as climate change and population growth take hold, the scientists said.

"There's not much chance here for spring-run (salmon) in the mainstem Sacramento River," said biologist Bruce Oppenheim. "We just don't have as much water available in Shasta in the future."

The discussion took place before an independent panel of scientists conducting a peer review of the findings for the CalFed Bay-Delta Authority, a joint state-federal agency charged with improving the Delta.

The meeting was highly technical but offered warnings about four protected species: winter- and spring-run salmon, Central Valley steelhead and green sturgeon.

Similar conditions exist in the American River: not enough cold water or habitat for steelhead spawning.

"By the time May comes around, it's really not a suitable place for egg incubation," said biologist Brian Ellrott.

Providing more cold water for fish would mean saving water behind dams for spawning season. This could mean less water for farms and cities in summer and fall.

Under the current system, risks to the fish are numerous. The Bureau of Reclamation, for instance, operates giant gates on the Sacramento River near Walnut Grove to divert freshwater into the interior Delta to freshen supplies available to diversion pumps.

When these gates are open, young salmon migrating to sea stray into waters teeming with predators, including foreign species such as striped bass.

Federal biologist Jeff Stuart said closing the gates almost doubles salmon survival rates.

Other threats include herbicides to control aquatic weeds, entrapment in the suction effect of the water diversion pumps, and rough handling at fish screens near the pumps.

"Basically, if you enter the interior Delta, you're not going to survive," Stuart said.

The biological opinion does not directly consider effects on fall-run chinook salmon, because this species is not yet protected by the Endangered Species Act. But it is declining steeply and affected by the same threats.

The fall-run remains the largest salmon population on the West Coast, vital as ocean-going adults to the commercial fishing industry. It's also a primary food for the southern resident population of killer whale, or orca, an endangered species that ranges from Puget Sound to Monterey. Fewer salmon spawning in Central Valley rivers, then growing into adults in the ocean, could mean hard times for the orca.

Maria Rea, Sacramento supervisor for the Fisheries Service, said her team has not finished evaluating whether California water operations threaten the orca.

Call The Bee's Matt Weiser, (916) 321-1264. To comment on Delta issues, visit our reader forum at www.sacbee.com/delta.