So many salmon once spawned each year in the Central Valley that humans all but lived on them, and chemical traces of the fish are still detectable in the soil, where the scavenged carcasses fertilized riparian vegetation.
“It was a salmon-based ecosystem,” said Peter Drekmeier, the policy director of the group Tuolumne River Trust.
All that has changed. California’s Chinook population has collapsed. The fish compete against agriculture, urban growth and climate change, and with their inland habitat mostly gone and the cold water they need to spawn a scarcer and scarcer resource, wild Chinook, especially in the San Joaquin River, face extinction. So do several other fish species, whose estuary habitat has been destroyed or drained dry by agricultural diversions. Reduced flows and higher water temperatures also cause frequent blooms of toxin-producing algae and cyanobacteria in the Sacramento–San Joaquin Delta—events that turn the water an electric green and which scientists consider serious threats to public health.
Environmentalists say the San Joaquin watershed needs more water. So do state officials, who in 2018 ordered water users to give a large share of water back to the San Joaquin and its tributaries, notably the Tuolumne.
But the fight to restore this ailing ecosystem has turned political, and environmentalists leading the effort are facing an unlikely foe—the water service provider for one of the most liberal cities in the country. The San Francisco Public Utilities Commission owns and operates O’Shaughnessy Dam, the cement wall built across Yosemite’s Hetch Hetchy Valley in the early 1920s. The dam gave birth to Hetch Hetchy Reservoir, the main water supply bank for 2.8 million people in San Francisco, the Peninsula and the South Bay. While the State Water Resources Control Board’s plan requires the utilities commission, as well as irrigation districts, to leave 40% of the San Joaquin River watershed’s total, or unimpaired, flow in the river for the benefit of fish, wildlife and water quality, the water users aren’t cooperating.
They refused to abide by the order when it was issued in late 2018, and in May, the City of San Francisco and the PUC sued the state to squash their river revival plan. The May 13 lawsuit argued that “there is little evidence that the flow conditions [called for by the state] will, in fact, materially protect native fish and wildlife”—a claim that biologists and environmentalists are quick to challenge.
The plaintiffs also took an unlikely political stance by embracing a recent change to the Clean Water Act initiated by the Trump Administration, which stripped state governments of much of their power to protect watersheds from energy development projects. President Biden is considering reversing the new rule, which weakened the State Water Board’s ability to oversee management of Hetch Hetchy.
Most scientists studying the watershed, its vanishing fishes and its plague of algal blooms say the system needs more water. They say current conditions have turned the Delta into a warm-water ecosystem in which species like introduced catfish and black bass will thrive but from which salmon, Delta smelt and green sturgeon will dwindle or disappear.
“[The San Joaquin River] cannot regain its ecological integrity and provide sustainable salmon fisheries without more flow,” the Department of Fish and Wildlife’s Water Branch Chief Scott Cantrell wrote in a 2013 letter urging the Water Board to increase the river volume to 60% of its unimpaired flow. Years of negotiations ensued, and in 2018, the Water Board settled on a compromise of 40%, within a 30% to 50% range.
But even the 40% compromise is more than water users want to swallow. Steven Ritchie, the SFPUC’s assistant general manager for water, says that for all practical purposes, there is not enough water in the Tuolumne watershed to meet the state’s requirements without unfairly impacting the PUC’s customers. San Franciscans already use relatively little water, and Ritchie says they would need to reduce current water use by half or more in order to provide the Tuolumne with 40% of its unimpaired flow.
Michael Cooke, a water policy expert with the Turlock Irrigation District—which along with the Modesto Irrigation District shares rights to the Tuolumne’s water with the SFPUC—says impacts to farmers “would be severe” if water users met the Water Board’s requirement.
Cooke and Ritchie say they and their agencies are willing and ready to help restore the river, and to this end they’ve offered up their own measures—part of a larger, basin-wide process called the “Voluntary Agreements” resolution. This program would ostensibly restore the Central Valley’s aquatic ecosystems, but environmentalists have widely criticized the Voluntary Agreements for lacking rigor, direction and a basic timeline for completion.
They also, generally speaking, lack water. The proposed actions of this alternative plan lean on habitat improvement measures, with just a relatively small amount of flow added back to depleted rivers.
“River flow is not the only variable,” Cooke said. “There’s also habitat, predators, Delta conditions, ocean conditions … . That’s why we’re looking at other strategies than just pouring more water into the system.”
The water districts have argued for culling populations of nonnative predator fish to help salmon, though an independent scientific review, ordered by the National Marine Fisheries Service, concluded this would be less beneficial for salmon than allowing more water down the river.
The districts have also offered to restore small parcels of floodplain where juvenile salmon find food and shelter. Research shows that access to inundated floodplains significantly increases the odds of a young Central Valley salmon surviving its migration to the ocean. But the total proposed floodplain habitat is almost negligibly sparse—80 scattered acres along a 50-mile section of river.
There is also some question whether these restored acres will even flood.
“You can restore floodplains, but if there isn’t water to activate them, they won’t work,” Drekmeier said.
Jon Rosenfield, a senior scientist with the environmental watchdog group San Francisco Baykeeper, said water flow in a river is “the master variable” that ultimately determines how effective other measures, like habitat improvements and predator control, can be.
“Nothing can substitute for flow,” Rosenfield said.
To the frustration of Tuolumne’s advocates, the SFPUC and the communities it serves have given feeble pursuit of alternative water sources. A recycling plant now under construction will produce between 2 and 4 million gallons of water per day—a scant fraction of the commission’s daily demand of about 200 million gallons. A few other recycling projects are in development, but significant inputs of recycled water are many years away. By contrast, the Orange County Water District is nearing completion on a plant that will produce more than 100 million gallons per day.
For the SFPUC, this means that giving water back to the Tuolumne River would cut directly into the urban supply. According to Ritchie, the state’s water quality plan would require the SFPUC to forfeit 93 million gallons every day to the river.
The SFPUC’s Voluntary Agreement proposal, he said, would be much easier on customers’ taps; it would mean giving up about 15 million gallons per day on average. This water would be released into the lower Tuolumne in the form of so-called “pulse flows”—water freed from dams in strategic bursts intended to give out-migrating salmon smolts a boost.
“We think that’s a more effective approach,” Ritchie said.
The water would be recaptured again and diverted to farmers before entering the San Joaquin—a curious add-on to the plan that environmentalists say ignores the needs of downstream users, and the fact that the out-migrating salmon are trying to reach the ocean, not just the San Joaquin River.
The pulse flow strategy relies on predicting when Chinook salmon smolts are leaving the river system—something Rosenfield said cannot be done reliably. The Central Valley’s Chinook, he said, evolved to utilize a widely diversified array of behavioral traits—among them migration timing. What this means is, schools of young salmon are swimming downstream almost constantly for several months in the spring. Short pulse flows, by design, would miss most of the fish.
“Once the pulse ends, those fish that didn’t get out of the river at the ‘right’ time are sunk,” Rosenfield said. “And, as it turns out, you can’t serve enough fish with any one short pulse to provide an adequate bump in survival—we’ve done the math on this.”
From February through June 21 of this year, the Tuolumne River in Modesto ran at an average 13% of the watershed’s unimpaired flow. Greg Reis, a hydrologist with The Bay institute, said such numbers are typical for the wet months, when nearly all rainfall and snowmelt is captured in reservoirs. The percentage of runoff in the river rises in the summer months, but only because total water volume in the watershed declines. The Tuolumne is now flowing at a trickle, and elsewhere in the Central Valley, river levels are dropping and temperatures rising. Salmon will soon be spawning, and experts, watching temperature forecasts, predict massive egg kills.
Historical hydrology graphs show a close link between river flows and fish numbers. In 1985, 40,000 Chinook salmon spawned in a single year in the Tuolumne, and in 2000, 18,000 salmon returned. Each of these Matterhorn-like spawning spikes came one three-year Chinook life cycle after extremely rainy winters, when rivers flowed high. On the flipside, extreme droughts have been followed by sharp dips in salmon abundance. In 1980, 559 salmon returned to the Tuolumne, 77 spawned in 1991 and 113 came back in 2015.
That fish need water is an inconvenient truth for California’s agriculture industry. For years, farming interests have argued that the Central Valley’s beleaguered river ecosystems need improved habitat, pollution and predator controls, and better fishery management in the ocean—basically everything except significant increases in water flow, even for rivers that have been pumped nearly dry.
But a wealth of research from state and federal agencies, universities, organizations and even irrigation districts, which find themselves bound by law at times to conduct environmental studies, shows otherwise—especially that juvenile salmon survival increases as river flows are elevated in combination with habitat improvements, and that predator control efforts are relatively ineffective unless higher water flow is incorporated. One 2013 “Predation Study” commissioned by the Turlock and Modesto irrigation districts—the SFPUC’s Tuolumne partners—found that large increases in the Tuolumne’s flow, as high as 2,100 cubic feet per second, dramatically increased the odds that tagged salmon released upstream would pass hydrophone stations lower in the river. At flows between 280 and 415 cubic feet per second, relatively few of the fish were detected and were presumed eaten by predators.
“They didn’t like the results, so they downplayed it,” said Chris Shutes, a water policy specialist with the California Sportfishing Protection Alliance.
He said that water users have repeatedly extracted favorable data from such studies which give the impression that adding water to depleted rivers is either insignificant or harmful. In fact, closeup views of the numbers can show that. The same study found that increasing the river’s flow within the lower end of the range led to slightly reduced survival of young salmon—possibly because very small fish can be swept downstream, and often past predator ambush points, by higher flows if there are no inundated floodplains to utilize. Shutes said that floodplains along the Tuolumne become inundated at about 1,700 cubic feet per second, meaning that flow increases beneath that threshold can be detrimental. In mid-June, the Tuolumne River flowed at barely above 100 cubic feet per second.
Barry Nelson, a Berkeley environmentalist who has fought to protect the ecosystems of the Central Valley and San Francisco Bay for three decades, said San Francisco’s water provider is twisting data to meet its own interests and, in doing so, helping drive “a wave of extinctions in San Francisco Bay.”
“The SFPUC is denying science in the same way the tobacco and the oil industries denied the science about cancer and climate change,” he said.
Federal law mandates salmon recovery. The Central Valley Project Improvement Act of 1992 includes a requirement for agencies to rebuild salmon and steelhead runs to something resembling their historic abundance. The Water Board’s flow requirements—and, ostensibly, the Voluntary Agreements—are intended to meet this goal. For the Tuolumne River, the target is to produce 38,000 adult fish in the ocean. Roughly half those salmon might eventually swim upriver and spawn, completing their legendary life cycle—still just a fraction of historic highs.
“It’s very doable,” Rosenfield said.
His organization, meanwhile, is not just thinking about fish. Along with the Stockton environmental justice group Restore the Delta, Baykeeper tracks harmful algal blooms. These episodes have grown more frequent in the past decade. Globally, they present a phenomenal mystery, almost certainly related to warming trends, and a challenge for waterway managers and health officials.
In the Delta, upstream diversions are probably fueling the HABs, as they’re often called, since lower flows often mean higher temperatures and nutrient concentrations. The blooms can turn water neon-green and produce toxins that linger and spread, even migrating into saltwater after the HABs subside. Rosenfield says cyanotoxins traced to Delta blooms have been found in San Francisco Bay, and emerging evidence shows the same toxins can go airborne and even harm human health through unexpected pathways—notably by tainting food crops grown with polluted irrigation water. The Delta is the water supply hub for tens of millions of people, and it is feasible that the toxins could find their way into municipal water supply systems. New research shows a strong link between certain algal toxins and liver cancer, and possible associations with Parkinson’s and Alzheimer’s diseases.
In the Delta, harmful algal blooms are a nuisance and a menace to swimmers, boaters, pets and, in general, all 330,000 people in the City of Stockton.
“I was just at the Stockton waterfront, and there is a bloom spreading right now,” said Barbara Barrigan-Parrilla, executive director of Restore the Delta, in mid-June. For years, she says, her group has encouraged state agencies as well as the SFPUC to increase reservoir releases to improve water quality in the Delta, as well as to protect the water supply that is pumped to Los Angeles.
“They’ve heard from us, they’ve read our letters, they know we’re concerned—but they just don’t think protecting Delta communities from harmful algal blooms is a worthy cause,” she said.
When asked whether such downstream consequences of the commission’s water withdrawals merit more conservation on the PUC’s customers’ part, Ritchie said no.
“Asking our customers to put more water in the system so that people in Southern California and other places have improved water quality doesn’t seem like an equitable solution to us,” Ritchie said.
San Francisco residents have shown themselves willing and eager to conserve water to help the environment. During the last drought, the city’s residents cut their water use by billions of gallons. However, these conservation efforts didn’t help the Tuolumne River or communities downstream at all. With less water flowing from city taps, more water remained in Hetch Hetchy Reservoir, where the SFPUC kept it. While San Francisco residents left their toilets yellow and their lawns brown, and while thousands of residential wells ran dry in the San Joaquin Valley, the commission hoarded its surplus water many miles upstream from the river’s salmon habitat.
“The PUC didn’t share any of the water with the environment,” Nelson said. “San Franciscans conserved during the drought, but it had zero benefit for the environment.”
By the end of the drought, after salmon experienced near-total spawning failures in the Central Valley, the SFPUC had a reservoir filled with water. Only when the wet winter of 2017 drenched the state with torrential rains and flooding did the PUC open the gates and flood the river.
Drekmeier remembers that winter.
“The Tuolumne was beautiful,” he said.
Now, as drought wrings the state dry, ecological needs have fallen last in line for water.
“They starve the river in dry years,” Drekmeier said.
