California’s disappearing salmon

The drought, along with man-made impediments, has
placed the state’s wild Chinook population at grave risk.

Story by Scott Wilson

Text-Only Version below, click the Here for the full version on The Washington Post’s Website

Videos and photos by Melina Mara

Sept. 13, 2021

HELLTOWN, Calif. — The name doesn’t seem to fit this quiet place set above a gentle swerve in Butte Creek, just an old span of bridge, some rusted-out mining equipment manufactured before this state was officially a state, and a seldom-used house.

But the harsh reality becomes apparent quickly, a smell on a hot, thin wind.

It is the stench from piles of rotting Chinook salmon carcasses on the creek banks and from the upside-down bodies of others snagged, already dead, on the creek’s pale rocks.

In a year with severe drought and record high heat in the West, many dead Chinook salmon have been found decomposing on the shores of the Butte Creek in Chico, Calif.

For centuries, spring-run Chinook salmon, among California’s most iconic fish, would rest for weeks in these historically cold waters after their brutal upstream journey. Then they would lay eggs and, finally, perish to complete one of nature’s most improbable life cycles.

No longer. What once was a place where life began is now one of untimely death.

The creek is simply too warm, an astounding 10 degrees warmer than average in some parts of these spawning grounds. It is the result of the creek’s low flow, which speeds up the spread of disease as the water stagnates, and of the Central Valley’s high heat in the depths of drought.

Of the estimated 16,000 spring-run Chinook that made the journey from the Golden Gate Bridge to this curve in a creek and others like it across the Central Valley, about 14,500 have died, nearly all of them before spawning. More will succumb in the next few weeks, and a year of spring-run Chinook reproduction will be lost in the valley’s hot, low-flow waterways. The conditions are threatening the winter migration, or “run,” just as severely. And while it is still too early to measure the drought’s effect on a pair of fall migrations, experts are worried it could be just as disastrous.

LEFT: With decreased water levels and warmer temperatures, rivers and creeks have lower oxygen content, which weakens and kills the fish before they spawn. RIGHT: Of the estimated 16,000 spring-run Chinooks that made the journey from the Golden Gate Bridge to creeks across the Central Valley, about 14,500 have died, nearly all of them before spawning.

“This year has been huge in terms of pre-spawn mortalities,” said Colin Purdy, the state Department of Fish and Wildlife’s environmental programs manager for fisheries based in the city of Chico. “This fall we’ll just hope to see enough juveniles get out to sustain the population, and we need enough adults to survive to help us avoid a failed class.”

[Severe heat and drought the hallmarks of a changing west]

The drought is enveloping much of the American West, where many places recorded their hottest July in history last month. The parched-brown landscape has become more normal than aberration in California, where the increasingly rapid shifts from cool to hot, wet to dry, are driving historically huge wildfires, deadly mudslides and new demands on water supplies.

Along with thirsty crops, dried-out wells and mounting economic loss across the state’s agricultural heartland, the drought’s second desiccating year is also punishing California’s rich wildlife, from migratory birds to bears and elk looking for a drink.

In a state that has historically been brutal to its mascots, from the extinct California grizzly bear that graces the state flag to the ever-on-the-brink condor, the Chinook is now threatened as never before by disruptive human engineering and the dangerously evolving climate.

“The salmon are basically like a canary in the coal mine, giving you some idea of what’s going on in the freshwater system,” said John McManus, who runs the Golden State Salmon Association, an advocacy group. “As go the salmon, so too go many other species.”

Drama in the gravel

People fish for trout on the Upper Sacramento River in Redding, Calif., in August.

Chinooks hit the rushing Sacramento River and its many tributaries in a ritual migration that shows that many salmon return to the exact same spots to spawn as their ancestors.

The Sacramento River, wide and swift, is the world’s only habitat for winter-run salmon.

Thousands of Chinooks leave the frigid Pacific in December to begin a roughly 325-mile swim upstream to waters that, for millennia, have been cooled by the melting snow and ice of the Sierra snowpack. This year the snowpack was roughly half its annual average.

The journey takes the fish — most nearly three feet long at this point — to the marshy and sometimes misleading canals of the Sacramento-San Joaquin River delta. Then they hit the rushing Sacramento River and its many tributaries in a ritual migration that shows that many salmon return to the exact same spots to spawn as their ancestors.

The problem, exacerbated severely by drought, is that the salmon would travel farther, much farther, but no longer can.

The Shasta Dam, completed in 1945, cut off the salmon from the snowmelt-cooled lakes and rivers farther north. Those included the now out-of-reach McCloud River, flowing a steady chill for nearly 80 miles through Shasta-Trinity National Forest.

LEFT: Cormorants frolic in pools on the Upper Sacramento River. RIGHT: A Western pond turtle sits along a bank of the Butte Creek.

Other vast federal and state water projects also have severed salmon from their home habitats. Nearly every river or creek system in the state’s Central Valley is dammed or diverted in some way, part of the engineering system that improbably allows 40 million people to live in the state, most of them in near-desert conditions.

In the valley, the government has spent tens of millions of dollars to build around these obstacles for wild-run salmon, including fish ladders and traps that lift the fish by elevator up and over dams. The state Department of Fish and Wildlife moved nearly 18 million salmon from protected Chinook hatcheries, which are essentially supporting the salmon industry here now, between April and July to remove them from rapidly warming river water. Some were released in creeks, others trucked to the sea — their survivability uncertain given the early release.

Water flows through a fish ladder during the salmon migration, or “run,” on the Upper Sacramento River.

But despite the government spending money and the success of some of the projects, the Chinook population continues to decline.

A long-term recovery plan now under discussion is “reintroducing” the winter-run Chinook to stretches of river above the Shasta Dam — an expensive and little-leeway operation given the salmon’s already endangered population.

“Our modeling projects that [the Sacramento River] is going to get too warm, and that a very large proportion of our juveniles this year just will not make it,” Jason Roberts, a state Department of Fish and Wildlife environmental program manager for inland fisheries, said of this year’s estimates.

Out on the river, Roberts points out places where, free of the current, Chinook carcasses collect, their decomposing bodies making the river murky in places and a census more difficult to undertake as a result.

Most of the dead fish on the Sacramento River had spawned. But a state Fish and Wildlife checkup on the winter-run Chinook last month showed a far higher than usual pre-spawn death rate.

LEFT: A slow-moving Chinook salmon navigates the Upper Sacramento River with sores on its body. RIGHT: A California Department Fish and Wildlife checkup on the winter-run Chinook salmon in August showed a far higher than usual pre-spawn death rate. This one died in the Butte Creek.

From 2003 to 2020, years when the state went in and out of drought, the average rate of winter-run Chinook dying before laying eggs was 1.3 percent. The recent agency survey found the rate this year to be as high as 23.3 percent. The proportion has decreased in recent weeks, but it is still more than double the average pre-spawn death rate.

“The drama now is in the gravel,” said Ryan Revnak, a Fish and Wildlife environmental scientist, as he looked toward the rocky river bottom. “Right now there are thousands and thousands of juveniles in the gravel where it is still cool enough for them to survive. But our fear is that they will all emerge into water that is way too warm.”

The river goes wild quickly once its passes by Chico. A trio of river otters appear on the banks at one point, diving quickly into the current once spotted.

Hawks and eagles glide overhead, and turkey vultures take up prime locations to pick up the dead salmon once they float to the surface. Some large Chinooks languish near the river’s shady edges, waiting to die.

When the state began tracking the winter-run Chinook population in 1970, there were more than 40,000 salmon making the sea-to-Sacramento River migration. The census last year found 80 percent fewer winter-run Chinook making the trip. The winter run is now classified as endangered.

“We expect that the survival conditions for the juvenile fish as they make their way out to the ocean is going to be really poor,” said Howard Brown, a senior policy adviser with the National Oceanic and Atmospheric Administration. “Things look really dire for winter-run Chinook.”

A California Department of Fish and Wildlife biologist holds a counted and tagged dead Chinook salmon along the Upper Sacramento River.

Canada geese walk up a screen and the fish ladder along the Butte Creek.

The push-pull between farmers and environmentalists over water is as old as the state. But it is in times of severe shortage when the discussions are most fraught. Water is a zero-sum resource in this state, now in the second year of a drought that began just a year after the last one ended.

Thousands of farmers in the Central Valley — home to the state’s lucrative and politically powerful $42 billion-a-year agricultural industry — have already been ordered by government regulators to refrain from drawing to the same degree on rivers where they have had rights for generations.

In a grim historic first last month, the federal government declared a water shortage in the Colorado River, cutting off thousands of people in Arizona and Nevada from that crucial supply. California could be affected by the order if the drought persists.

Already many of this state’s reservoirs are at dangerous, even historic lows, including the nearby Shasta Reservoir on the Sacramento River, which provides a third of the state’s water demand and is now holding water at a quarter of its capacity.

A salmon jumps in a cool pool of the Upper Sacramento River.

Given the gravity of the drought, state and federal officials have worked successfully with some agricultural interests on agreements to delay drawing some of their traditional water allocation from the federal Depression-era Central Valley Project and the State Water Project until later in the year.

This will, in theory, keep the river flows as high as possible for salmon runs through the fall, which helps allow the fish to find colder water at depths and prevents the disease that comes with water stagnation. But it has come at a cost to farmers, with some deciding to fallow fields and others planting less acreage up and down the valley.

“A lot of the rivers and streams dried up earlier than we had seen before, and what that means is basically we are in a situation now where we’re relying entirely on water that’s in storage,” said David Guy, president of the Northern California Water Association, which represents water districts, water companies, farmers and small towns with interests in water allocation decisions. “That inevitably involves trade-offs. It involves some hard decisions about water use.”

Guy’s association represents farmers working a combined 2 million acres of crops in the Central Valley, some more water-intensive than others.

Many of his members rely on the state and federal aqueduct systems and well water to grow a variety of crops — from rice to walnuts, row-crop beans to almonds. Last year alone, the California almond crop was estimated to be worth more than $6 billion. Guy’s association also has a program to preserve the wild salmon runs, which this year he said has been a large focus of his membership and state agencies.

But Guy also believes the state is at times being too protective and shortsighted with its salmon population, given that agriculture is the economic driver in the region.Those decades of Central Valley water-related construction included periods of drought — the most severe was in 1976 and 1977 — and salmon have managed to rebound after each.

LEFT: Kaitlin Whittom, of the Pacific States Marine Fisheries Commission, measures the depth of salmon pools on the Upper Sacramento River. RIGHT: Jessica Nichols, the state biologist, works on the fish ladder along the Butte Creek.

“There’s the doom and gloom, and then there’s the fact that this is an amazingly resilient species,” Guy said. “And I don’t know how they do it. But, man, they are survivors.”

The difference now, environmentalists warn, is the frequency and severity of the droughts, the quick spring onset of heat, the evaporation of vital snowmelt before it hits the rivers, reservoirs and streams, and the continuing increase in human population and water demand.

And while farmers have found ways to become more efficient with water use in recent decades, the agriculture industry is still using more water than any other industry in California — about 40 percent, by some estimates — and more water than is allocated officially for river and stream flow, according to several state agencies.

“It’s incumbent on Californians to make a decision now about what kind of future they want,” said McManus, the salmon association president, who once was a commercial salmon fisherman in Alaska. “Do they really want to see species blink out of existence so that a handful of major agriculture operators can continue to produce at a really large scale?”

Struggling to survive to die again

Allen Harthorn, founder of Friends of Butte Creek, walks among the small percentage of surviving Chinook salmon.

The heat and lower-flow waterways due to drought have created tepid, often near-stagnant pockets of creek where disease spreads rapidly among the fish. Those diseases are the main cause of the sky-high mortality rate.

To get to Helltown, you pass the charred valley walls of a canyon where a pair of major wildfires have burned in the past several years, evidence that this bend in the river is in many ways at the center of California’s shifting climate.

Small, weedy islands appear in the Butte Creek flow here. They are submerged in years of normal rainfall and runoff that does not evaporate in the late spring heat.

High in the hills are large — and probably illegal — marijuana farms growing a water-intensive crop that state officials fear may be drawing off the creek. Black bears have been seen far more frequently along the creek banks, gorging on the dead fish.

“We just can’t have back-to-back bad years here,” Colin Purdy, the state Department of Fish and Wildlife’s environmental programs manager for fisheries, based in Chico, said of the Butte Creek.

“Even in really good years, we manage the survival of these fish right on the edge of disaster,” said Brown, the NOAA adviser. “In a drought like this, we’re seeing water temperatures go up to very high levels. And that ends up killing them.”

The drama here in this Sacramento River tributary involves the adults, not their offspring.

Purdy, the environmental program manager for fisheries, said there were signs of hope as the spring run made its way north this year. There were more of them than in some recent years.

But the rain never came, and the snowmelt did not deliver.

Unlike their winter-run counterparts who arrive and spawn soon after, the spring-run Chinook linger for months, through much of the summer, in what is usually the creek’s 55-degree water.

The creek temperature today is roughly 10 degrees higher than that, and it is a natural impediment — a churning mix of waterfall and rapids called the Quartz Bowl — that prevents the spring-run salmon from seeking cooler water farther north.

The heat and lower-flow waterways due to drought have created tepid, often near-stagnant pockets of creek where disease spreads rapidly among the fish. Those diseases are the main cause of the sky-high mortality rate.

“It’s pretty hard on the staff who are working and tracking and trying to take care of these fish,” Purdy said. “Our hope is to have between 500 and 1,000 fish surviving through the end of the season.”

LEFT: Kaitlin Whittom and Jamie Chelberg, from the Pacific States Marine Fisheries Commission, take their measurements on the Upper Sacramento River. RIGHT: Jason Roberts, left, program manager at the California Department of Fish and Wildlife, and biologist Matt Johnson search for Chinook salmon on the Upper Sacramento River.

The salmon here live on a three-year cycle — from birth, through the journey to the sea, and then back again to spawn and die. As a result, the full consequences of this year will not be evident for another few. At the time of the 1976 drought, the spring-run Chinook census was 25,141 fish. Three years later the number was 2,866.

“We may have very few adults here in three years from now,” Purdy said. “We just don’t know how many juveniles will be born and how they will do once they reach the ocean.”

Here, too, it’s not only death on display. What else is evident is a salmon’s intense survival instinct.

A few Chinook salmon swim in a cool pool in the Butte Creek.

A roughly three-foot Chinook swings its tail gently, just enough to keep it in place as it faces upstream for easier breathing. The fish swims in water so shallow that its tail crests the river surface.

Soon it will join the fresh Chinook carcass caught up in the tangle of branches that line the creek. Or wash up with the longer-dead, now in blackening piles along the islet in the middle of the creek.

Or it will simply flip over and die, before its time, as one did just a few feet from where the Chinook is making its last stand against the will of a changing climate and the audacious engineering of man. From a 1982 peak, when 25,980 made the spring run, the spring-run Chinook population had dropped to 1,688 by the end of last year.

“We just can’t have back-to-back bad years here,” Purdy said. “We have so little leeway. And if we do have another year like this, we will come very close to the extirpation of this population.”