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Conservationists say time running out to save endangered salmon in Sacramento River - San Francisco Chronicle

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As the extreme drought causes various agencies to squabble over dwindling water supplies, conservationists say the state is still not doing enough to prevent an endangered run of salmon from dying in the Sacramento River.

At issue is how the federal Bureau of Reclamation manages water flows from Shasta Lake into the Sacramento River, which is both the spawning grounds for chinook salmon and the main water source for Central Valley farms. If the bureau releases too much water to irrigation districts, the river level could drop low enough and warm enough to kill off 50% of the eggs of endangered winter-run chinook salmon, the ones that migrate from the Pacific in winter and spawn from April to August.

Those conditions could also harm the fall-run chinook that are part of the commercial fishery, which migrate in fall but spawn soon after the winter-run. But if more water is kept in the reservoir, more cold water can be released over the summer and fall when fish spawn.

The State Water Resources Control Board recently told the bureau it needs to have at least 1.25 million acre feet of water in Shasta Lake at the end of September. But salmon advocates say that amount is too low because it wouldn’t leave enough cold water to release in the river and would result the egg kill-off.

“What’s been proposed by the state water board in their recent letter fails to adequately protect salmon and also leaves very little water in storage in case next year is also dry,” said Doug Obegi, senior attorney at Natural Resources Defense Council. A state order requires the bureau to maintain a temperature below 56 degrees in the river south of the reservoir to protect eggs from the various salmon runs, and the water board has the authority to oversee how the bureau manages temperatures.

Obegi and other conservationists say the state should require water storage of at least 1.47 million acre feet — even that would result in mortality of 32% of this year’s winter-run salmon eggs, according to the National Marine Fisheries Service.

That would be an improvement over what happened in the last drought, when 95% of winter-run chinook salmon eggs and young fish died because of warm Sacramento River water in 2014 and 2015.

The target of 1.25 million acre feet was reached “after extensive coordination, analysis and information sharing” between the bureau, the state Department of Water Resources, and state and federal fisheries agencies, Eileen Sobeck, water board executive director said in a statement. This week, the board is expecting a final plan from the bureau on how it intends to maintain temperatures of 56 degrees in the spawning area.

“We believe that this target represents a reasonable balance between temperature control this year, maintaining some carryover storage going into next year, and providing for consumptive water supply needs,” Sobeck added.

A group of senior water rights holders called Sacramento River Settlement Contractors, composed mostly of irrigation districts, has agreed to voluntarily reduce its diversions to meet the goal of maintaining 1.25 million acre feet of water storage in Lake Shasta by September, said Thaddeus Bettner, manager of Glenn-Colusa Irrigation District, its largest contractor.

“Obviously conditions will keep changing as we go,” he said. “We’ll keep having to adapt with the end goal of trying to achieve that storage.”

Bettner said reducing releases to the degree conservationists are asking for would force more farmers to dial back production.

“Where does that hit get absorbed? We’re trying to manage the different trade-offs that exist,” he said.

Spawning Sacramento winter-run salmon are already being affected by warm water the bureau has been releasing recently near the surface of the reservoir to save cold water for later.

As of May 21, 25 adult fish were found dead before spawning after river temperatures surpassed 61 degrees, according to the California Department of Fish and Wildlife, which described “live fish that are exhibiting unusual swimming behavior, fish covered with fungus patches and unspawned fish drifting downstream while still alive but moribund and presumed to die shortly after observation.”

The temperature in the river has since gone down, but the stressful conditions could lower the reproduction success of adult survivors, said Jon Rosenfield, senior scientist at the conservation group San Francisco Baykeeper.

In recent state water board meetings, many California tribal members have also urged action to save salmon, in light of previous mass die-offs during drought.

Morning Star Gali, a tribal water organizer for the nonprofit group Save California Salmon, called native people’s inability to access salmon “cultural genocide” since it was a mainstay of their diet before so many of the state’s rivers were diverted and dammed.

“We should be doing everything possible at this time for our salmon to be able to be healthy, because that is our essential fight,” she said.

Tara Duggan is a San Francisco Chronicle staff writer. Email: tduggan@sfchronicle.com Twitter: @taraduggan

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