The drought’s hidden victim: California’s native fish

Fish culturalist Beau Hopkins stores winter-run salmon eggs after counting them at the Livingston Stone National Fish Hatchery north of Redding, Calif.
(Brian van der Brug / Los Angeles Times)

Last summer, a narrow, rock-rimmed stretch of the Sacramento River near here turned into a mass graveyard for baby salmon.

Upstream releases of water from Shasta Dam were so warm that virtually an entire generation of endangered winter-run Chinook was wiped out. The eggs never hatched, or if they did, the emerging young soon died.

A similar disaster could unfold this summer. And if the drought drags on for another year or two, wild populations of some of the state’s most prized fish are likely to vanish.


“We’re going to be losing most of our salmon and steelhead if things continue,” said UC Davis professor emeritus Peter Moyle, a leading authority on California’s native fish. Also in danger are the long-suffering delta smelt, whose numbers have plunged to what he called “the last of the last.”

“It would be a major extinction event,” Moyle warned.

The drought’s toll on California has been measured mostly in terms of idled cropland, dried up domestic wells and brown lawns. Less visible but more devastating has been damage to native fish that struggle for survival in the best of times.

Four years of drought — and the accompanying relaxation of environmental standards by state regulators — have compounded the harm of dams and diversions that long ago thwarted fish migration and destroyed habitat.

Spawning winter-run Chinook would never choose to hang out on the outskirts of Redding on a day when the city baked in 111-degree heat. They would prefer to swim in the cold, spring-fed waters of the McCloud and other Sacramento tributaries to the north.

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But for about 70 years, those historic spawning grounds have been out of salmon reach, blocked by the towering concrete face of Shasta and the buttresses of its smaller sibling, Keswick Dam.


“This is as far as fish can go on the Sacramento main stem,” fishery biologist Ryan Revnak said as he steered his boat upriver toward Keswick, which regulates flows from Shasta’s hydropower plant.

Revnak, who works for the Pacific States Marine Fisheries Commission, pointed out the gravel beds where the salmon built their nests, called redds. A female, close to death after laying her eggs, hovered in shallow water near the bank. A dead male, his procreative work also done, floated by.

Salmon eggs and emerging fry need cold water to survive. The river temperature shouldn’t top 56 degrees. Last year in the spawning grounds below Keswick, it climbed above 62 degrees. Only 5% of the 2014 brood stock lived.

The U.S. Bureau of Reclamation, which operates the dams, had miscalculated the volume of cold water in Shasta and didn’t have enough to maintain the proper river temperature. The problem wasn’t just that the drought had slashed runoff that fills the lake; the computer model used to predict cold water storage was wrong.

Federal agencies are trying to avoid a repeat this year by rationing Shasta’s cold water releases so managers don’t run out while the eggs and young develop over the next few months. But stretching the cold water reserves has meant lower releases this summer, nudging up the river temperature a degree or two during peak spawning.

And long bouts of 110-degree days in Redding could further warm the river. “There’s a lot of uncertainty” in the plan, said Maria Rea, assistant regional administrator for National Oceanic and Atmospheric Administration Fisheries. “I don’t have a high confidence that it will work.”


If it doesn’t, an industrial-looking complex near the base of Shasta Dam could be the winter run’s last hope.


One wall of the Livingston Stone National Fish Hatchery is lined with incubation trays holding hundreds of thousands of winter-run eggs and young in different stages of development: fertilized eggs, eyed eggs that resemble pink jelly beans with two miniature fish eyes, sac fry feeding on their yolks, tiny infant fish that wiggle like a mass of gray worms.

Tanks of juveniles fill the main building. Adults are held in outside tanks, enclosed in zippered tents so they can’t leap out.

Livingston is a conservation hatchery, opened in the late 1990s to maintain a genetically diverse population of wild winter-run. In a typical year, the hatchery traps up to 120 returning adults in the Sacramento and spawns them with the precision of a champion horse breeder.

The average female lays 5,000 eggs, which are divided into two or more sets. Each set is fertilized with sperm from a different male whose DNA has been analyzed to avoid inbreeding.


The tanks and egg trays are bathed with circulating water released from the dam. Last summer, hatchery managers had to use chillers to maintain the proper temperature. They may have to do the same this year.

To counter the drought losses, Livingston has ramped up production. The hatchery team is spawning 300 adults this year and come winter will release twice as many juveniles into the Sacramento as it normally does.

But even in good years, only a tiny fraction of those young hatchery salmon survive to adulthood and return to spawn. And if river conditions aren’t right, their offspring will perish.

Facing that grim scenario, Livingston last year established a captive brood stock, which the hatchery will raise for the entire three-year life cycle of the fish. If worse comes to worst, it will function as a fall-back population. “You can’t give up trying,” said Assistant Hatchery Manager John Rueth.

In the meantime, he added, “All of us keep praying for this massive El Niño.”


About 90 miles to the south, Carson Odegard and Justin Fairchild put on wet suits while standing on the back of a pickup truck parked not far from the DeSabla Powerhouse in upper Butte Creek Canyon. They walked for a mile on catwalks atop an old water flume, then descended to the creek on an oak-studded slope covered in brush and so steep the pair had to use ropes on the hike down.


They were ready to start their weekly snorkeling survey of another run of salmon that the state Fish and Wildlife Department is nervously monitoring.

Butte is one of only three tributaries of the Sacramento River where wild populations of the once bountiful but now threatened spring-run Chinook can still be found.

The Butte group is by far the largest. But this spring, biologists counted only 1,950 “silver bullets” as they passed through a Chico fish ladder on their way upstream, where the salmon hold until they start spawning in late summer. It was one of the lowest counts since the 1990s, when government agencies launched a restoration program that has so far poured $50 million into improving fish passage and habitat.

The number dipped even lower in June, when several hundred salmon died after a lower stretch of the creek hit lethal temperatures. Now there are about 1,500 spring-run waiting to spawn. Most are in a few remote miles of the Butte, downstream of a deep pool formed by a quartz-streaked rock bowl.

Fairchild, a Chico State environmental sciences graduate in his third summer on the Butte, and Odegard, a Chico State biology student, cover the most arduous part of the 11-mile snorkeling survey: the upper 2 miles. “There’re a couple of guys who hate this section,” said Fairchild, referring to others on the crew who prefer to work the tamer, downstream portions.

The pair jumped about 15 feet off a rock ledge into the pool, fed by a narrow chute of tumbling white water that acts as a natural barrier to migrating fish.


They swapped out the data logger in a thermograph that records the pool temperature every 30 minutes, and then swam downstream, searching for salmon carcasses. They take notes on waterproof paper, and if they encounter a carcass they take tissue samples for lab analysis. This day they came across no dead salmon, a good sign.

State Fish and Wildlife scientist Clint Garman has worked on the Butte project for 16 years. He consults weekly about creek conditions with other government biologists and the Pacific Gas and Electric Co., which diverts water from the west branch of the Feather River into Butte to boost hydropower production.

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With Central Valley heat climbing into the triple digits last month, they decided to increase releases of the cold river water to try to keep the creek temperature out of the danger zone. (The June die-off occurred when PG&E temporarily shut down the diversion to repair a leaking canal.)

After mid-August, overnight temperatures in Butte’s upper drainage start to drop and the team can relax a bit.

In a state as extensively plumbed as California, the fate of fish can be more dependent on water managers than nature. As the drought has deepened, state and federal water officials have repeatedly pushed regulators to relax flow and water quality requirements to free up more supplies for agricultural and urban use.


In response, the State Water Resources Control Board has issued a dozen such orders for just the Sacramento-San Joaquin Delta — even as the numbers of some delta fish species have crashed to record or near record lows.

Officials of the reclamation bureau, which delivers water to Central Valley growers, say they sought the changes to balance demands for shrinking supplies and to keep water in upstream reservoirs. Releasing more flows in the spring to help delta fish “would have just hammered those storage levels and we would have been in an even worse [situation] coming into the summer,” said Ron Milligan, operations manager of the Central Valley Project.

Environmental groups have protested the changes and recently filed a lawsuit to reverse them.

“I’m despondent about the impacts we’re seeing. Delta smelt are as close to extinction as you can be without being extinct,” said Jon Rosenfield, a conservation biologist with the Bay Institute.

“I know there’s pain in the ag sector,” he said. “But it’s temporary. If we lose salmon or delta smelt … it will have permanent consequences.”
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