There may not be tumbleweed blowing through the salty streets of California’s coastal marinas, but the collapse of the state’s Chinook salmon runs has reduced many ports to ghost towns. 

At Bodega Bay, Sausalito and other seaside harbors, fishing boats that once targeted the coveted fish have been idled for almost two years after officials determined there are not enough salmon off the California coast to support harvest.  

Once abundant, Chinook have been devastated by habitat loss, water diversions from the rivers where they spawn and drought. They are trending toward extinction. And while recovery is a possibility, it will be an upstream push. The salmon need improved spawning grounds and more floodplain nursery habitat. 

They also need more cold water. And in 2023 and 2024, both exceptionally wet years, they got it—until, that is, they didn’t. Water temperatures in the middle Sacramento River soared to lethal levels this spring, exceeding basic environmental objectives and threatening salmon born last summer and fall. 

With no agency taking firm ownership of the problem, the mishap raises the question of who’s at the wheel in managing the state’s reservoirs and rivers for fish and who’s to be held accountable if salmon disappear.

The temperature troubles can be traced upstream to Shasta Dam, which creates California’s largest reservoir. The lake is almost full – typically a great boon for fish downstream. However, Lake Shasta is also unusually warm this year, according to local irrigation districts, which say this has produced similar temperature profiles downstream of the dam. 

Fishery advocates frame the story differently. They say the warm water spike in May was an avoidable outcome of water management decisions, and they’re blaming officials for prioritizing human water supply over basic environmental needs.  

“It’s a violation of state law, and they know they’re doing it,” said Tom Cannon, a retired fisheries ecologist and consultant. 

He says the U.S. Bureau of Reclamation, with the approval of state regulators, released so much of Lake Shasta’s water through the spring to Sacramento Valley farmers that keeping water cool enough to protect migrating salmon smolts, then ocean-bound, became impossible. 

Environmentalists also accuse the State Water Resources Control Board—the top water referee in the state—of setting weak temperature standards in the first place and failing to enforce them. If this continues, they say, the fish may never recover. 

“They are managing salmon to extinction,” said Tom Stokely, a water policy consultant for the group Save California Salmon.  

Through the spring, the Bureau of Reclamation released several heavy bursts of water from Lake Shasta to help salmon born last summer and fall migrate downstream. These so-called “pulse flows”—recommended by federal endangered species rules—first exit Shasta Dam, then run through a smaller facility called Keswick Dam, and finally course through miles of meandering river channel. 

But between pulse flows, the river has dropped dramatically. During such lulls, water temperatures predictably jump. In mid-May, a gauge at a site called Wilkins Slough registered 72 degrees Fahrenheit—surpassing a state limit of 68. Such warm water is dangerous for small salmon, making them sluggish and predator fish more active. 

Fishery advocates say the 68-degree objective, ordained by the state water board’s “Basin Plan,” could have been achieved without disruption if the Bureau of Reclamation had slightly reduced water allocations to valley farmers. 

But the Bureau of Reclamation—which operates Keswick—claims no responsibility.

“Reclamation does not manage Keswick Dam releases for water temperatures at Wilkins Slough,” a staff member explained in an email. He elaborated that water outflow from the dam is used to meet water supply demands and keep salty ocean water at bay, away from the major pumping stations in the southern Sacramento-San Joaquin Delta. 

These facilities, which send water to millions of people and vast farming regions, were the site of another recent controversy when the pumps exceeded “take” limits on protected winter-run Chinook and steelhead trout. In spite of complaints that thousands had been sucked to their deaths, the Bureau of Reclamation has not entirely mitigated the entrainment. 

This month, the agency reported an “increasing” trend of steelhead found at the pumps. These fish are usually rescued alive, but their presence is an indicator of other fish that were not so lucky.

To Jon Rosenfield, science director with the group San Francisco Baykeeper, such losses in a wet year bode poorly for the species’ futures.

“If they’re making decisions that cut against the fish in 2024, when reservoirs are full and many contractors are receiving full deliveries, is there a year when they won’t harm imperiled fish species?” he said.

Shasta is one of many California dams from which water releases harm fish. Coyote Valley Dam, on the Russian River, is another. 

A court ruling in early May found that the U.S. Army Corps of Engineers has violated the federal Endangered Species Act for years by releasing muddy water from the bottom of Lake Mendocino, through the dam and into the Russian River. These flood control releases, according to a lawsuit filed in 2022 by private citizen Sean White, cloud the river with silt and sediment and harm the watershed’s salmon and steelhead, all nearly extinct.   

There is, however, good news emerging on the horizon for California’s troubled salmon. The water board recently approved the Bureau of Reclamation’s 2024 Sacramento River temperature management plan. This planning document, which features projections of the reservoir’s stored water and its temperature by depth, shows that water releases will remain cold through the fall, leading to minimal losses of fertilized salmon eggs. This would be a promising turnaround from recent years when most eggs of spawning salmon were killed by temperatures in the mid-to-high 50s.

State and federal water officials are tasked with a tricky balancing act of providing water to people while protecting the environment. In many cases, contractual obligations to deliver water to farmers weigh heavily on the agencies. So do rules meant to protect fish. Both sides take hits when supplies run low.

But the treatment is not always equal, and the agencies often bypass environmental regulations to better supply farms and cities. 

In the wet winter of 2023, Gov. Gavin Newsom signed an order allowing the state water board to waive basic environmental flows in the Delta so agencies could store more water in reservoirs. Many similar waivers were made in prior years—often through a regulatory tool called a temporary urgency change petition—allegedly killing millions of fertilized eggs and smolts and possibly precipitating the Chinook’s collapse. 

While 2023 and 2024 are shaping into a decent time for the Central Valley’s salmon, it could have been a great one, owing to the abundant water and snowpack it produced.  

“Mother Nature gave us two good years in a row,” Rosenfield said. “We need to rebuild the population that was decimated during the last few drought years.”

Rosenfield wants to see a systematic increase in average river flows through the Delta, all the way to the ocean. While this would likely benefit struggling species, it’s a divisive idea since it would mean reducing Delta water exports. 

“There are a few groups that always point to the farmers whenever they believe there’s a water need for the fishery,” said Lewis Bair, the general manager of Reclamation District No. 108, which provides water to Sacramento Valley farmers. 

Bair says unusually warm water in Lake Shasta has made it difficult to meet the physiological needs of Chinook salmon, even though the reservoir is nearly full. 

“It’s unheard of to have a reservoir this full and to have this temperature challenge,” he said. 

Climate change and warming trends, Bair said, existentially threaten salmon and steelhead. Saving them, he noted, will require expanding upstream spawning habitat and providing access to cold tributaries currently blocked off by dams. 

Environmentalists tend to agree. But many argue that state policies are just as dangerous as changing climate. Of particular contention is a rule known as Water Right Order 90-5, which sets a 56-degree threshold for spawning salmon in the Sacramento and also the Trinity River, a major Klamath tributary connected to the Sacramento basin by an 11-mile tunnel bored through the Coast Range mountains. 

That 56-degree limit is widely considered to be scientifically outdated and a potential death sentence for salmon eggs. In June, a group of organizations requested that the water board initiate a process of amending the rule by reducing the threshold to 53.5 degrees—what would align with federal endangered species guidelines.

Water board staff told Weeklys in an email that they plan to “assess this issue further” later in the year.  

Stokely isn’t holding his breath. He said he has been encouraging the board to amend the order for years. He and his allies in conservation want them to write in lower temperature limits for both the Sacramento and the Trinity, where coho salmon have recently suffered almost complete spawning failures.

“If they don’t change Water Right Order 90-5, we’re certainly looking at the end of salmon fishing and salmon in general,” Stokely said. “They’re on the road to extinction. They can’t go on like this.”