One of the last wild runs of chinook salmon in California is sinking fast amid the four-year drought and now appears perilously close to oblivion after the federal agency in charge of protecting marine life documented the death of millions of young fish and eggs in the Sacramento River. The National Marine Fisheries Service reported Wednesday that 95 percent of the winter-run chinook eggs, hatchlings and juvenile salmon died this year in the river, which was too warm to support them despite conservation efforts. It was the second year in a row that most of the juvenile salmon died in the soupy water released from Shasta Dam, failing to make it to the ocean. The situation could have far-reaching effects, leading to cuts in water allotments to farmers next year if projected rains and a strong snowpack don’t erase drought deficits this winter. Commercial and recreational fishing limits could be imposed to protect the endangered chinook population, taking a toll on those industries. “Certainly there is cause for alarm when we are talking about 95 percent mortality,” said Garwin Yip, the branch chief for water operations and delta consultations for the fisheries service. “We think it is temperature-related.” Not enough cold water The problem was caused by a lack of snow this year on top of four years of drought. The U.S. Bureau of Reclamation, Yip said, was left without enough cold water behind Shasta Dam to release during spawning season. Chinook, also known as king salmon, are born in the Sacramento River and pass through San Francisco Bay. They roam the Pacific Ocean as far away as Alaska before returning three years later to spawn. There are three distinct runs of salmon — winter, spring and late fall, which is what West Coast fishers catch in the ocean. The winter and spring-run chinook salmon are listed under the state and federal endangered species acts. The winter run has been endangered since 1994. The fisheries service worked with two state agencies, the Department of Water Resources and the Department of Fish and Wildlife, to develop an elaborate plan this year to regulate cold-water releases from Shasta Dam. Resource officials are required by law to release enough cold water to keep the Sacramento River at 56 degrees — the ideal temperature for fish. In a bid to meet that requirement, federal officials sharply limited flows and delayed water deliveries to hundreds of Central Valley farmers. Failed plan The problem, Yip said, was that “there wasn’t as much cold water as anticipated and the water wasn’t as cold as we thought it was going to be.” The lack of cold water forced regulators to come up with a new temperature management plan, this one allowing the water to warm up to 57 degrees. But it didn’t work, and water temperatures, at times, rose to 58 degrees, he said. As a result, the number of juvenile fish counted this month at the Red Bluff diversion dam, downstream of Shasta, was down 22 percent compared with last year, which was also a bad year. That’s despite the fact that there were 21 percent more adult fish laying eggs in the river, Yip said. Two months remain in this year’s run, but the number of juvenile fish is unlikely to grow much beyond the 217,489 counted so far. The dismal state of affairs is even more stark when compared to historic numbers. In 2005, officials counted 8.5 million winter-run juveniles, and there were 4.4 million juveniles in 2009, the year the winter-run salmon conservation requirements were drafted. Another bad year would mean that all three year classes of winter-run chinook are in peril, a clear sign that the species is heading toward extinction. “I think the message is that winter run, at least right now, aren’t doing too well,” Yip said. “The species can bounce back, but we’ve had drought conditions since 2012. It’s a caution that we are going to have to operate Shasta tighter and monitor releases more closely next year.” Salmon fishermen are alarmed about how the fish deaths might affect their industry next year, said John McManus, executive director of the Golden Gate Salmon Association, a major advocate for the state’s $1.4 billion salmon industry. “The real problem here is that water management policies in the Sacramento Valley and the delta are killing these winter-run fish,” he said. The Sacramento River’s spawning run is the last great salmon run along the giant Central Valley river system, which includes the San Joaquin River, where leaping, wriggling chinook were once so plentiful that old-timers recall reaching in and plucking fish right out of the water. The construction of Shasta Dam on the Sacramento, Friant Dam on the San Joaquin, Folsom Dam on the American River and Oroville Dam on the Feather River over the past century cut off huge sections of river, wiping out most of the fish. Today, mostly fall-run hatchery fish are caught in the ocean and river flows are regulated to protect the remaining wild fish, including winter-run salmon. That’s why the fate of juvenile salmon is so important. Reduced flows from Shasta this year required officials to increase releases from Folsom Lake, which reached record-low levels. The cascade effect increased the tension among farmers, water agencies and environmentalists throughout the Sacramento-San Joaquin Delta region.