Salmon advocates say they know how to restore sustainable salmon runs in the Central Valley – 26 different ways.

The Golden Gate Salmon Association says two years of study have resulted in a 26-project salmon rebuilding plan to reverse the steep decline of California’s four salmon runs, including two considered endangered and threatened under the Federal Endangered Species Act — the winter and spring runs.

The fall and late fall-runs, which support the sport and commercial fishery, declined by 90 percent and 87 percent respectively from 2001 to 2011, the association says.

“The salmon problems are not in the ocean but rather in the freshwater rivers where salmon reproduce and then try to migrate downstream through the many hurdles that exist on their journey to ocean waters,” says GGSA Chairman Roger Thomas.

The 26 projects are divided into three tiers to prioritize completion. In April the first eight high priority projects were selected with most underway or in the pipeline for 2014. The second tier is currently being considered by federal agencies for implementation.

The rebuilding plan can be broadly broken into two categories of projects, says the association. The first calls for better flows for salmon in the Sacramento and San Joaquin rivers and the Sacramento-San Joaquin Delta. The second are projects aimed at healing manmade structural impediments built in and along the rivers.

The loss of many baby salmon at the pumping facilities that divert water from the Delta for export south is another problem the GGSA says its plans address.

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With a flash of silver and pink, a male salmon signaled its arrival in a stretch of the Tuolumne River near La Grange.

It sought to fertilize eggs laid in the shallow stream bed gravel by a female that also had returned from a few years in the Pacific Ocean.

Chinook salmon spawning has been going on since September on San Joaquin Valley rivers. It’s a stirring sight for people who love nature, but important as well to farmers and other water users who could face cutbacks if the fish numbers stay low.

This year, at least, they are not doing too badly. Many of the spawning fish were born on the rivers in 2010 and 2011, when the water ran high, and they enjoyed healthy conditions at sea. They return to streams shrunken by drought, but well-timed reservoir releases have provided some of the flows they need.

“This is where they want to be,” said Gretchen Murphey, an environmental scientist for the California Department of Fish and Wildlife, during an early December visit to the La Grange stretch. “This is the habitat they’re looking for.”

As of Monday, 3,607 salmon had passed through a fish-counting device on their way to the Tuolumne’s spawning stretch in the low foothills, up from 2,152 a year earlier, and just 255 in 2009.

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The federal agency that regulates water releases from the Shasta Dam in Northern California drastically cut those releases in November, and one fisheries group is afraid that the move could have killed millions of eggs laid by fall-run chinook salmon in the Sacramento River below the dam.

According to the Golden Gate Salmon Association (GGSA), the U.S. Bureau of Reclamation (BuRec) cut releases from Lake Shasta from 6,000 cubic feet per second (CFS) to 3,750 CFS between November 1 and 25. This caused river levels downstream to drop dramatically, which means that any salmon eggs laid in parts of the river that died up will almost certainly be lost.

This isn’t the first year BuRec has cut November water releases from the dam, and those cuts have hurt salmon in previous years. As many as 15 percent of the Sacramento river’s fall-run eggs were lost after a similar move in 2012, and almost a quarter of the run’s 2011 eggs were killed the same way, according to GGSA.

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