The Biden administration has adopted new rules for operating California’s main water delivery systems in the Central Valley, endorsing a plan backed by state officials that aims to strike a balance between ensuring protections for imperiled fish species and providing a reliable water supply for farms and cities.

Federal and state officials said the new operating rules for the Central Valley Project and the State Water Project that were developed over the last three years will bring greater stability to the state’s supplies in the face of worsening droughts intensified by climate change.

“The updated rules mark a new path forward that will provide more certainty for water users, and fish and wildlife,” said Karl Stock, the federal Bureau of Reclamation’s regional director, calling it a “durable plan that builds in a great deal of flexibility.”

The staff of several federal and state agencies developed the revised plan after California and environmental groups successfully sued to challenge previous rules adopted during Trump’s first presidency. The new framework replaces court-ordered interim plans that were adopted during the last three years, but long-running disputes over California water management are far from settled.

Environmental and fishing groups said the new rules fail to provide adequate protections for threatened and endangered fish species in the Sacramento-San Joaquin River Delta. Agricultural water districts raised other criticisms. And President-elect Donald Trump, who has pledged to deliver more water to farms and cities, is widely expected to again seek to revamp California water management.

Having the new plan “helps lock things in” for the time being, said Greg Gartrell, a former manager of the Contra Costa Water District. “If the new administration wants to change it, they’re going to have to go through a big process to do it, and that’s going to take a few years.”

Gartrell said he expects there will also be a new round of lawsuits.

Some initial legal challenges have already begun. Last month, a group of agricultural water districts sued state agencies to challenge their approval of the rules for the State Water Project and a related permit for the “incidental take” of threatened species caused by pumping facilities. Westlands Water District, the largest supplier in the Central Valley, said there are unresolved questions about how operations of the state and federally managed systems will be aligned.

“We are disappointed by the truncated and incomplete process” that led to the rules, said Allison Febbo, Westlands’ general manager. The process was carried out on a “rushed timeline,” she said, and failed to address “critical issues brought forth by key stakeholders.”

Water from the Delta is pumped to cities throughout Southern California, and the region’s largest supplier supported the plan. Deven Upadhyay, interim general manager of the Metropolitan Water District of Southern California, said the plan provides “regulatory stability” that is crucial for water management.

Federal officials defended their process, saying they met legal requirements, convened many meetings and incorporated extensive input. The plan is based on “true collaboration, dialogue and science,” said Jennifer Quan, regional administrator of National Oceanic and Atmospheric Administration Fisheries.

The rules took effect last week as the federal Bureau of Reclamation approved the plan and the supporting biological opinions, which determine how much water can be pumped and how river flows are managed in the Sacramento-San Joaquin River Delta. The rules govern the operations of dams, aqueducts and pumping plants in the Central Valley Project and the State Water Project, two of the world’s largest water systems, which deliver supplies to Central Valley farmlands and about 30 million people.

Withdrawals of water by the massive pumps that feed the systems have contributed to the ecological degradation of the Delta and San Francisco Bay, where threatened and endangered fish species include steelhead trout, two types of Chinook salmon, longfin smelt, Delta smelt and green sturgeon.

Federal officials said the changes under the new rules include provisions aimed at managing cold-water reservoir releases from Shasta Dam to help endangered winter-run Chinook salmon survive. Other provisions focus on an “adaptive management” approach that will allow managers to incorporate new scientific findings.

Shasta Dam, part of the Central Valley Project, towers above the Sacramento River near Redding.

(Max Whittaker/For The Times)

Deciding how to manage these water systems is “among the hardest of natural resource issues west of the Mississippi,” said Charlton “Chuck” Bonham, director of the California Department of Fish and Wildlife. He said operations of the two systems had been divided in recent years and “forced into conflict,” but now are closely aligned under the rules.

“Chaos hurts,” Bonham said. “Avoiding chaos, getting alignment and moving forward together, against the face of a hotter and drier future, is the benefit of doing these operational rules the way we’ve done them.”

He said some “screaming and yelling” can still be expected over the plan, but that the process was thorough and not rushed.

“The reality is it’s not political,” he said, describing the plan as an effort to “find the right balance” that will be “good for both people and for the environment.”

Announcing the new rules on Friday, state and federal officials said one key goal was making the management framework flexible to adapt to climate change. Paul Souza, regional director of the U.S. Fish and Wildlife Service, pointed to recent scientific findings that the last 25 years have likely been the driest quarter-century in 1,200 years in the American West, and that global warming is driving more intense droughts.

“We know that our fisheries are in great decline,” Souza said. “So thinking through how we manage the resources we love with a hotter and drier climate is really important, and this is a step forward.”

Souza said the “adaptive management” provisions bring additional flexibility to the operations, and will allow for managers to decide based on the latest science, for example, whether fish populations would benefit from the release of a “pulse of water.” He and other officials also touted the inclusion of proposed negotiated agreements in which water agencies have pledged to forgo certain amounts of water while also funding projects to improve wetland habitats in an effort to help fish species and the ecosystem.

Gov. Gavin Newsom, who is promoting plans for the construction of Sites Reservoir and a proposed $20 billion water tunnel in the Delta, praised the new framework as an important step toward improving management and making the state’s water systems more resilient.

“We know what the future has in store for our state: hotter hots and drier dries,” Newsom said. “That means we have to do everything we can now to prepare and ensure our water infrastructure can handle these extremes.”

However, environmental advocates said the protections for imperiled fish species are inadequate.

“These rules are somewhat better for the environment than current operations, but not good enough to satisfy legal obligations, let alone allow for species and ecosystem recovery,” said Ashley Overhouse, water policy advisor for the group Defenders of Wildlife.

Jon Rosenfield, science director for the group San Francisco Baykeeper, said the federal rules fail to improve conditions for seven fish species that are rapidly declining toward extinction. He said he expects the Trump administration will try to further weaken “this very weak set of protections.”

Environmental groups have also been calling for the State Water Resources Control Board to adopt strong regulatory standards as it considers options for updating its plan for managing flows in the Delta.

Trump has said that water in California is “horribly mismanaged” and has indicated he wants to weaken 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.”

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

California’s coastal fishing industry depends heavily on catching fall-run Chinook salmon. But with the fish population struggling after years of severe drought, officials have shut down the salmon fishing season the last two years.

Those in the fishing industry have blamed water managers for decisions that they argue have deprived rivers of the cold flows salmon need to survive.

Scott Artis, executive director of the Golden State Salmon Assn., said the Bureau of Reclamation’s actions have had devastating effects on salmon in recent years. While the new plan includes a “few modest improvements,” he said, “it’s not near enough.”