LOS ANGELES — The Biden and Newsom administrations will soon adopt new rules for California’s major water delivery systems that will determine how much water may be pumped from rivers while providing protections for imperiled fish species.

But California environmental groups, while supportive of efforts to rewrite the rules, are criticizing the proposed changes and warning that the resulting plans would fail to protect fish species that are declining toward extinction in the Sacramento-San Joaquin River Delta and San Francisco Bay.

As the preferred proposal is laid out in a federal draft environmental review, the new rules “would make things worse,” said Jon Rosenfield, science director for the group San Francisco Baykeeper.

“We are deeply concerned that six endangered species in the Bay Delta are on the verge of extinction or headed in that direction,” Rosenfield said.

The rules under revision govern dams, aqueducts and pumping plants in California’s two main water systems, the Central Valley Project and the State Water Project, which deliver water to millions of acres of farmland and more than 25 million people. Pumping to supply farms and cities has contributed to the ecological degradation of the Delta, where threatened and endangered fish species include steelhead trout, two types of Chinook salmon, longfin smelt, Delta smelt and green sturgeon.

The rewriting of the rules, along with supporting biological opinions, began nearly three years ago after California and environmental groups successfully challenged the Trump administration’s previous rules in court, arguing that 2019 biological opinions failed to provide adequate protections for endangered fish.

Federal and state agencies are now aiming to lock in new rules in the coming weeks amid uncertainty about the presidential election, which in the event of a victory by former President Donald Trump would likely bring new attempts to weaken protections for fish.

“The Biden-Harris administration and the Newsom administration, which said that we’re going to do better than the illegal Trump administration plan, have actually produced a less protective plan that will accelerate the path to extinction for many of these fish species,” Rosenfield said. “No doubt a Trump administration would seek to weaken these protections, but that is not an argument to lock in obviously inadequate protections.”

State officials disagreed, saying their plan for the State Water Project will better protect fish species.

The state Department of Water Resources has been working for the last several years with the U.S. Bureau of Reclamation and counterparts at state and federal fish agencies to complete a new permit — called an incidental take permit — for the State Water Project, said Karla Nemeth, the department’s director.

Nemeth said DWR’s proposal for operating the system “includes a portfolio of actions designed to reduce impacts to listed species while ensuring water supply reliability amid a changing climate.”

That permit for the State Water Project is separate from the forthcoming biological opinions for the federally operated Central Valley Project.

Nemeth said state officials are working with federal partners to ensure the rules governing operations of both systems “are aligned to benefit listed and endangered fish species while continuing to provide water to millions of Californians.”

The development of the new operating rules has involved more than 21/2 years of consultations and analysis through a “multi-agency state and federal team with regular engagement and opportunities for feedback,” said Mary Lee Knecht, a spokesperson for the Bureau of Reclamation. She said the proposal focuses partly on “striking a reasonable balance among competing demands for water, including the requirements of fish and wildlife, agricultural, municipal, and industrial uses of water.”

The time allotted for updating the rules is coming to an end. For the last three years, federal and state officials have operated the water systems under a court-ordered interim operations plan, which will expire in December.

The federal environmental review — called a draft environmental impact statement— includes several alternatives, and environmental groups have urged officials to consider one that they say would provide stronger environmental protections than the Biden administration’s preferred alternative.

Trump has said in recent campaign speeches that water in California is “horribly mismanaged” and that if he is elected, he would deliver more water to farmers and cities. He has indicated he would again seek to weaken environmental protections, lamenting that because of “a little tiny fish called a smelt, they send millions and millions of gallons of water out to the Pacific Ocean.”

Vice President Kamala Harris, in contrast, would likely seek to maintain stronger environmental protections.

Such arguments over water in the Delta have long pitted Central Valley farmers and agricultural water districts against environmental groups, fishing advocates and Native tribes.

The California Farm Bureau, the state’s largest agricultural organization, raised various concerns about the proposed rules in a recent letter, saying the federal analysis ignored the fact that farms face state-mandated limitations on groundwater pumping in the coming years.

Alexandra Biering, the Farm Bureau’s senior policy advocate, wrote in the letter that agricultural water users have been frustrated by “politically driven regulatory uncertainty” and have been “left in a limbo of sorts about the future operational conditions of the projects” as officials have pushed for rewriting the rules.

“I continue to be dismayed about the fact that this is a political football, and it just keeps getting kicked from one side to the other,” Biering said in an interview. “Everybody wants to lock something in before the potential for a change in administration, which I understand, but I think it inevitably leads to this perception that politics is what’s driving those decisions.”

That’s unfortunate, she said, because the same public officials have been tasked with revising the plans for years under different administrations. Biering said she’d like to see the process be “a little bit more insulated from politics.”

Large urban water agencies that depend on the State Water Project have also been weighing in.

Adán Ortega Jr., board chair of the Metropolitan Water District of Southern California, said leaders of the agency would like to see state and federal permits “that have consistent terms across them.” He said the district, which supplies water for 19 million people, supports the inclusion of proposed negotiated agreements — called Agreements to Support Healthy Rivers and Landscapes— in which water agencies have pledged to forgo certain amounts of water while also funding projects to improve wetland habitats.

Those proposed deals, also called the “voluntary agreements,” have been supported by Gov. Gavin Newsom and his administration but strongly opposed by environmental groups, who have argued this approach would mean reduced flows in the Delta and would be detrimental to fish and the ecosystem. Instead, they have called for science-based flow requirements to help fish populations recover.

“The science is very, very clear, and has been for a long time, that without additional flows into, through and out of the Delta to San Francisco Bay, these species will continue to decline,” Rosenfield said.

Another key water policy framework is now being developed by the State Water Resources Control Board, which on Friday released a draft review of potential options for updating the state’s plan for managing flows in the Delta. It includes options for incorporating the voluntary agreements proposal.

The state water board has not yet decided which option it will adopt in the updated Bay-Delta Plan. Board members will hear comments from the public at a series of meetings in November, December and January.

The board has not set a date for adopting the plan but is aiming for sometime in summer or fall of 2025, said Eric Oppenheimer, the board’s executive director.

Whatever approach the board ultimately takes, legal challenges are expected.

Potential litigation also looms as the federal government finalizes the rules for operating the Central Valley Project. Environmental groups have said the Biden administration’s preferred plan is built on the controversial voluntary agreements, and the analysis failed to properly assess the environmental effects of two proposed infrastructure projects — Sites Reservoir and the Newsom administration’s plan to build a $20-billion water tunnel — both of which the groups are fighting.

A coalition of environmental groups raised other concerns in a recent letter, condemning the federal government’s proposed rules for excluding environmental impacts on the Trinity River and its fish. The groups said that “creates an overestimate of the water available for export” and will result in uncertainty and potentially more litigation.

“They’re going to make it worse for fish in California,” said Tom Stokely, water policy adviser for the group California Water Impact Network.

Max Gomberg, a former state water official who resigned in 2022 over differences with the Newsom administration, said the proposed rules would “essentially maintain the status quo,” which has harmed the Delta’s ecosystem and fisheries, and would allow “environmentally destructive levels of water exports.”

“The only real beneficiaries are a few wealthy Central Valley growers,” said Gomberg, a board member of the California Water Impact Network.

State officials disagreed with the claims that the proposed rules would be less protective of the environment.

“We believe the proposed State Water Project operations will better protect threatened fish species by incorporating new science and addressing climate change impacts,” said Ryan Endean, a spokesperson for the Department of Water Resources.

He said the improvements partly come through commitments to restore marsh and floodplain habitats, as well as other efforts to support the recovery of fish species.

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