SACRAMENTO — In the latest break between the Trump administration and California on environmental policy, officials decided Tuesday to give the state unprecedented control over a water plan that delivers water to more than 27 million residents.

For decades California and the federal government have collaborated on rules intended to supply farmers, fish and cities with enough water to survive the state’s boom and bust rainy seasons. As managing partners of California’s intricate water infrastructure — the feds largely keep farmers’ fields green while the state focuses on parched cities like Los Angeles and San Diego — the two sides routinely cooperated on a framework to ensure the survival of Chinook salmon and other endangered species.

The federal government operates the Central Valley Project and California manages the State Water Project, with both sourcing water from the drainage point of the state’s largest rivers in the Sacramento-San Joaquin River Delta.

But under President Donald Trump’s administration, the seemingly solid relationship has crashed and the sides are now suddenly setting their own playbooks when it comes to California’s prized water supply.

The feds initially reviewed the impact of their proposed changes to fish species such as salmon and smelt in July 2019 and concluded excess water deliveries to farmers would harm the populations of imperiled species. But the administration pulled that document within two days of its publication and two months later reversed course by claiming it was possible to increase farmers’ take without killing fish.

Last month, Trump traveled to California to make good on a campaign promise to “open up the water” to Central Valley farmers and inked the plan critics warned was a death sentence for the state’s iconic species.

“As a candidate for president, I promised to help solve the water crisis that was crippling our farmers due to the chronic mismanagement and misguided policies,” Trump said, taking a shot at California water managers and environmentalists.

California responded one day later and slapped the Trump administration with a lawsuit challenging the new biological opinions. It believes the lax pumping requirements could result in a lack of fresh water for fish during the summer and fall.

With communication and cooperation at a standstill, California on Tuesday for the first time issued a new operating permit for its water project without guidance from the federal government.

The heads of the state’s natural resources agencies defended the move in a joint statement, claiming it was necessary to install new pumping limits in order to protect salmon.

“California’s water operations need to support our communities while protecting our fish and wildlife,” said Department of Water Resources Director Karla Nemeth and Department of Fish and Wildlife Director Charlton Bonham. “Most importantly, it ensures that our state water infrastructure operates in a manner protective of fish species listed under the state’s endangered species law. It does so in many ways, including by dedicating water for delta outflows during drier periods when fish and habitat need it the most.”

According to the state, the incidental take permit relies on new scientific data and modeling and will provide a sorely needed update to old laws governing when and how much water can be pumped out of the delta. It says the goal is to make the water system more flexible and allow up to an additional 250,000-acre feet of water to be released during the spring and summer when conditions are right. The State Water Project delivers an average of 2.9 million acre-feet to its contractors annually.

Meanwhile, environmental groups have been critical of both the government pumping plans.

A collection of groups including the Natural Resources Defense Council, Restore the Delta and California Sportfishing Protection Alliance argue the state plan does not accurately account for climate change impacts like brackish water and reduced river flows. They have long fought for stricter pumping limitations and roundly oppose the state’s permit.

“Climate change sensitivity analysis is likely not sensitive enough to the effects of climate change,” the groups wrote to state regulators. “The environmental impact report provides no sea-level rise analysis for long-term operations of the State Water Project as it would affect delta operations.”

Doug Obegi, an attorney with the Natural Resources Defense Council, says the state’s version fails to protect the delta’s ecosystem and is likely to spark litigation.

“I expect that conservation and fishing groups will be forced to go to court to challenge these unlawful decisions, in order to prevent these species from being driven extinct and to protect the thousands of fishing jobs that depend on a healthy delta,” Obegi wrote in a blog post late Tuesday.

Public water agencies, including Friant Water Authority which operates a 152-mile canal in the Central Valley, echoed Obegi’s prediction of new court battles.

Jason Phillips, Friant CEO, called the state’s decision to disregard the feds’ biological opinions “disappointing.”

“While we are still evaluating the full impact of the state’s permit, we fear the inconsistency with the federal opinion and the failure to acknowledge the best available science will throw California’s water operations into a tailspin, causing unnecessary disruptions to the operations of the Central Valley Project and State Water Project,” Phillips said in a statement. “It’s very difficult to envision a path forward that doesn’t include litigation, public bickering and finger-pointing, and water shortages and uncertainty for family farms, disadvantaged communities, and municipalities throughout the San Joaquin Valley and elsewhere in California.”

As is often the case in California, the courts will ultimately have a major say in determining how much and often water should be pumped out of the delta. But for the time being, the sides are planning to abide by two sets of rules regardless of the confusion that may come. “Operating to different criteria creates challenges for both real-time operations and seasonal and long-term planning,” the Bureau of Reclamation warned in January.

— By Nick Cahill