California’s water wars escalated Thursday, as state leaders vowed to fight the Trump administration over plans to ship more water to Central Valley farms.

Gov. Gavin Newsom and members of his administration announced that they were preparing a lawsuit against the federal government to prevent California’s rivers and wildlife from being cheated out of vital supplies.

State leaders said boosting agricultural deliveries, a longtime campaign promise of the president, could upend fragile watersheds and threaten such protected fish as the iconic chinook salmon and delta smelt.

While California has been quick to challenge the Trump administration on many fronts, from immigration to air pollution, the thorny issue of water has been one that Newsom hasn’t wanted to stoke. The first-year governor instead has generally pursued a middle ground between the environment and big water users allied with Washington.

Thursday’s announcement signals a change of direction.

“We are once again marshaling our collective resources and building on our record of strong, science-based environmental policies, to chart a new path forward for water policy in California,” Newsom said in a prepared statement. “As stewards of this state’s remarkable natural resources, we must do everything in our power to protect them. The next generations of Californians deserve nothing less.”

At issue is the age-old question of how water should be allocated from California’s massive state and federal waterworks. Both the federally operated Central Valley Project and the State Water Project collect mountain runoff in giant reservoirs and send it downstream to cities and farms. As much as 30% of the state’s water is delivered through the two systems.

Last month, the Trump administration released new rules for both water systems, known as biological opinions, that loosen restrictions on water deliveries. Federal officials said the old policy was outdated and burdensome.

The administration’s changes were cheered by farmers in the San Joaquin Valley who have blamed long-standing environmental regulation for tying up water to the state’s $54 billion agricultural economy.

Environmental groups, however, blasted the rules. They said additional water releases would dry up the Sacramento-San Joaquin River Delta and the rivers that feed it, jolting a statewide ecosystem that supports not only fish but birds, bears, killer whales and other plants and animals.

The state’s planned litigation will take aim at the new biological opinions. Officials at the California Natural Resources Agency and the California Environmental Protection Agency said they were still working out details of the lawsuit but hoped to file it in the “coming weeks.”

Doug Obegi, a senior attorney at the Natural Resources Defense Council, was among the many environmental voices praising the state’s entry into the high-stakes battle.

“The federal plan is really a plan for extinction,” he said. “I’m glad to see the state stand up to the Trump administration. This is a big deal.”

Federal officials did not want to comment on a yet-to-be filed lawsuit but defended their position.

“From the beginning, we’ve been focused on cooperative solutions with the state of California to bring reliable water supplies to farms, families, communities and the environment,” Brenda Burman, commissioner of the Bureau of Reclamation, said in a statement. “Today’s announcement by Gov. Newsom is disappointing in his preference to have judges dictate these important projects instead of the career professionals at the federal and state levels who have developed a plan based on the best science and significant input from the public. If that’s their choice, we’ll see them in court.”

The state’s lawsuit probably would not be resolved before the new federal rules kick in, expected as soon as January, when a required environmental review is complete. State officials didn’t say whether they would ask the courts for a preliminary injunction. Such a request could prevent the biological opinions from taking effect until a judge rules on the case.

The state on Thursday also launched an effort to free the State Water Project from the federal water rules. The federal regulations have historically governed both the state and federal water projects in an effort to coordinate policy. The two governments use many of the same rivers and aqueducts to move supplies.

However, officials with the California Department of Water Resources said they now want the freedom to operate independently, agreeing with the environmental community that the biological opinions fall short of protecting rivers and wildlife.

The agency released a draft environmental impact report, the first step in what could be a months- or years-long process of establishing state rules for releasing water.

“This draft points to a more sophisticated and nimble way to manage the State Water Project to improve our ability to protect species and operate more flexibly,” said Karla Nemeth, director of the Department of Water Resources, in a prepared statement.

Despite the state’s new opposition to looser water rules, the Newsom administration said it is still committed to working collaboratively with big water users.

The governor has been trying to broker a deal behind closed doors between water users and environmental groups on the amount of water that should be left in California’s rivers. Newsom’s goal is to leave enough flows to maintain healthy ecosystems while appeasing the cities and farms that draw water.

A compromise has remained elusive, however, and Thursday’s moves by the state add a new layer of intricacy to the discussions.

Kurtis Alexander is a San Francisco Chronicle staff writer. Email: kalexander@sfchronicle.com Twitter: @kurtisalexander