The Sacramento-San Joaquin River Delta on June 22, 2023. (Photo by Miguel Gutierrez Jr., CalMatters)

The Bay-Delta Ecosystem Is Collapsing. California Just Unveiled Rival Rescue Plans

Back CalMatters Sep 29, 2023 By Rachel Becker, CalMatters

With the Bay-Delta watershed in the throes of an ecological crisis, California’s water regulators Thursday unveiled several controversial options for managing the heart of the state’s water supply

The long-awaited, nearly 6,000-page draft is part of a fiercely contentious but under-the-radar process to update the Bay-Delta Water Quality Control Plan, with high stakes for both wildlife and water providers serving cities and millions of acres of farms. 

State water officials have said that existing requirements for water quality and flow through the critical but imperiled San Francisco Bay and Sacramento-San Joaquin Delta watershed have “failed to protect fish and wildlife” and must be updated “to halt and reverse the ecosystem collapse.” 

Several of the strategies the report evaluates would set minimum amounts of water to remain in rivers and streams, which could ultimately require water suppliers and other water users to cut back on how much they divert for people and farms. 

Another approach assessed is a controversial pact that Gov. Gavin Newsom reached last March with major water suppliers, who volunteered to surrender some water and help restore habitat in the watershed. 

Next comes a gauntlet of workshops, hearings and public comment meant to help shape regulations that the State Water Resources Control Board likely won’t even consider adopting for at least another year. Once it does, it could take years to put the updated Bay-Delta plan into action. 

For the vast majority of the watershed, it’s already been 30 years since water officials made meaningful changes — a delay that has infuriated environmentalists, Native tribes, Delta-area residents and the fishing industry.

The draft report weighs several approaches to update standards for most of the Bay-Delta watershed, including the Sacramento River and its tributaries; the Mokelumne, Cosumnes and Calaveras rivers; and the San Francisco Bay-Delta itself. 

Spurred by inadequate flows, the loss of habitat and degraded water quality, native fishes are experiencing “prolonged and precipitous declines” in the watershed, state water regulators reported in 2018. Among the threatened and endangered: the winter-run chinook salmon and the tiny Delta smelt, a cucumber-scented indicator of the ecosystem’s health. 

Though the State water board said it remains agnostic for now about which of the strategies it will ultimately approve, the document devotes a lot of ink to discussing one that’s sort of a Goldilocks proposal when it comes to water flow — not the highest or the lowest, but in the middle. 

It calls for minimum flows of at least 55% of the amount of water that the rivers would have carried were they not dammed or diverted, resulting in an average of about 1.5 million acre-feet more water flowing out through the Delta, state water official Diane Riddle said at a media briefing. 

This water, which then couldn’t be exported south to farms and cities, would be enough to supply about 4.5 million households. 

That’s more than the flows that would result from the “voluntary agreements” deal reached by the Newsom administration and water suppliers, which results in about 500,000 to 700,000 additional acre-feet flowing through the Delta, according to Riddle — less in extremely wet or dry years.

A coalition of water suppliers — including the State Water Contractors, an association of 27 public water agencies — responded to the report with their strong support for these voluntary agreements. 

“These innovative agreements … will improve environmental conditions more quickly and holistically than traditional regulatory requirements, while providing more certainty to communities, farms, and businesses,” the coalition said in a letter to the board. 

But environmentalists say the voluntary agreements do not provide enough water to protect fish and wildlife. And tribes and environmental justice organizations said they were the result of backroom negotiations that excluded people of color, a complaint that the U.S. EPA is now investigating

Malissa Tayaba, vice chair of the Shingle Springs Band of Miwok Indians, said they were not given sufficient notice of the report’s release. “If they cannot get the process right, it creates a great deal of distrust for working through the substance, or lack of substance, within the Bay-Delta Plan itself for tribal concerns,” she said. 

Despite their dueling visions, both water suppliers and environmental organizations said it’s high time for the draft to be completed. 

“We’re glad to have this report, but it’s way too long in coming,” said Jon Rosenfield, science director at San Francisco Baykeeper. “Fish, wildlife, water quality and communities are suffering while the state dawdles on addressing major problems in its crown-jewel aquatic ecosystem.”

The Delta has long been the epicenter of some of the most turbulent water wars in California, and the Bay-Delta Plan touches many of them. Here’s more to know: 

Taking a toll on fish and fishing

Stretching from about Fresno to beyond the Oregon border, the vast Bay-Delta watershed drains water from about 40% of California. It’s formed by the Sacramento and San Joaquin river systems, which join at the Sacramento-San Joaquin River Delta and flow out to the Pacific through San Francisco Bay.

This critical water hub is where state and federal pumps move water from Northern California reservoirs south to help supply more than two-thirds of Californians with drinking water and irrigate millions of acres of agriculture. 

Delta smelt swim in a tank at the UC Davis Fish Conservation and Culture Laboratory on July 19, 2022. The Delta smelt is a small, slender fish that only lives in the Delta. Photo by Hector Amezcua/The Sacramento Bee via Reuters
Delta smelt swim in a tank at the UC Davis Fish Conservation and Culture Laboratory on July 19, 2022. The Delta smelt is a small, slender fish that only lives in the Delta. Photo by Hector Amezcua/The Sacramento Bee via Reuters

It’s home to more than 750 species of animals and plants, and is vital to the fishing industry, supporting about 80% of the state’s commercial salmon fishery. This year, for only the third time ever, California saw its commercial and recreational salmon season cancelled.

“Without healthy Bay-Delta salmon runs, we don’t have a healthy California salmon fishing industry,” said Barry Nelson, a policy representative for the Golden State Salmon Association. 

The culprits behind fish decline are many, including habitat loss, invasive species, and Delta water export pumps so powerful they can make rivers run backward. But a “significant contributing factor”, state water board staff reported in 2018, is the loss of water diverted for farms and cities, which reduces freshwater flows needed to keep water quality, temperatures and other conditions hospitable to fish. 

“The overall health of the estuary for native species is in trouble,” water board staff wrote five years ago, “and expeditious action is needed on the watershed level to address the crisis.” 

The last major updates for the Sacramento River and Delta were in 1995 

“Expeditious” is the last word most would use to describe the process of updating water quality and flow standards for the Bay-Delta. 

In 2018 the state water board adopted new standards for saltwater encroaching on the southern Delta and set flow requirements for the Lower San Joaquin, Stanislaus, Tuolumne and Merced Rivers. The update has not yet been implemented, and is already the subject of a dozen lawsuits. 

But for the rest of the watershed, aside from minor modifications in 2006, it’s been almost 30 years since the plan was updated. 

“I will acknowledge this has taken us longer to get to this point than we had all hoped,” said Eric Oppenheimer, chief deputy director of the state water board. While it was hard to ascribe a specific reason, he said, the droughts diverted personnel and attention. 

Environmental groups blame the delay on negotiations with major water users to develop those voluntary agreements. The agreements have been in the works since 2016 and have not yet been finalized. Riddle said the state board expects additional documents needed to flesh out the deal to be submitted by the end of the year. 

Even the federal government has urged state officials to move faster.

“EPA is concerned about the ongoing delays in completing revisions to the Sacramento and Delta portion” of the water quality control plan, Tomás Torres, water division director for  EPA Region 9, wrote to the State Water Board in January. 

Torres encouraged the state to “make decisions expeditiously now” and amend the plan later “should more specific voluntary agreements be developed in the future.” 

Why water agencies love the voluntary agreements, and enviros hate them 

Signed by powerful suppliers like the Metropolitan Water District of Southern California and agricultural providers like Westlands Water District, the U.S. Bureau of Reclamation and state agencies, the voluntary agreements take aim at the uncertainty of the regulatory process and the lawsuits that result. 

“There’s been fights and lawsuits about how much flow should go to outflow, how much flow should go to habitat, how much flow should go to cities and agriculture,” said Alison Febbo, general manager for Westlands Water District, a major Central Valley irrigation supplier. “And the (voluntary agreements) are trying to say, ‘Let’s stop that fighting. Let’s all work together and collaborate.’” 

Still, she said, there’s much to be hashed out. “If anybody leaves the table, it kind of falls apart,” she said. “I can’t say that Westlands is 100% completely supportive no matter what. We think it’s a good path. We think it’s the right way to go. But we have to see how it all turns out.” 

Environmental and fishing organizations said that habitat cannot be traded for water, and that the trade contradicts the state’s own science.  

“Habitat restoration is definitely necessary for some of these fish, but there is no solution to what ails the San Francisco Bay and its watershed that does not involve significant increases in flow,” Rosenfield said. “Flow controls all of the habitat conditions.”

State Water Board scientists agreed in a 2017 report, saying that “recent Delta flows are insufficient to support native Delta fishes for today’s habitats…Flow and physical habitat interact in many ways, but they are not interchangeable.”

Why the U.S. EPA is investigating

In 2022, the Shingle Springs Band of Miwok Indians’, Winnemem Wintu Tribe, and several environmental organizations including Stockton-based Restore the Delta filed a federal complaint with the EPA, saying that the state has allowed “waterways to descend into ecological crisis, with the resulting environmental burdens falling most heavily on Native tribes and other communities of color.”

Among their concerns: the state’s lengthy delay in updating the water quality standards, which the complaint says has worsened harmful algal blooms, low flows, and contamination — interfering with cultural, subsistence and recreational uses of the waterways for tribes and communities of color in the watershed. 

“Instead, the health risks of (harmful algal blooms) layer on top of outsized environmental burdens already borne by these communities,” the complaint says

The coalition asked the EPA to investigate and to develop its own water quality standards for the Bay-Delta. The board has said that it will cooperate with the investigation, and is weighing adding tribal and subsistence fishing beneficial uses to the Bay-Delta Plan. 

But Gary Mulcahy, government liaison for the Winnemem Wintu Tribe, said that’s not enough.

“There is something wrong when California Indians have to file a complaint with the Federal Government to protect our civil rights,” he wrote in a statement. 

“A Bay-Delta Plan without a tribal beneficial use plan, lack of tribal and community protections from harmful algal blooms, and adequate flows for the recovery of salmon (Nur) for our people means that the Board is not taking our just demands seriously.” is a nonprofit, nonpartisan media venture explaining California policies and politics. ​​

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