The rivers that once poured from the Sierra Nevada, thick with snowmelt and salmon, now languish amid relentless pumping, sometimes shriveling to a trickle and sparking a crisis for fish, wildlife and the people who rely on a healthy California delta.

A state plan to improve these flows and avert disaster, however, has been mired in conflict and delays. And critical opposition is coming from an unexpected place: progressive San Francisco. City water officials worry that the far-reaching effort to revive hundreds of miles of waterways will mean giving up too much of their precious mountain supplies.

Now, as the city water department works to defeat the state plan — pitting itself against environmental groups in an unlikely alliance with thirsty Central Valley farmers, as well as their backers in the Trump administration — some at City Hall have begun wondering if San Francisco is on the right side of California’s latest water war.

In a recent sign of an emerging divide, Supervisor Aaron Peskin is threatening to introduce a resolution that challenges the position of the San Francisco Public Utilities Commission and declares the city officially in support of the state’s river restoration.

“I’m concerned that the PUC is playing footsie with the Trump administration at the detriment of the environment,” Peskin told The Chronicle. “This is a city that prides itself on its environmental record, and we should be part of the solution.”

Whether Peskin’s measure could force the largely independent Public Utilities Commission to change course is unclear. So is the resolution’s chance of winning approval from the full Board of Supervisors.

Peskin’s colleagues and those at the water agency remain concerned that forfeiting water, under the state plan, would prompt mandatory water cuts and drive up water rates as the city is compelled to seek out new, pricey supplies, such as desalination.

But what is clear is that, even without a successful resolution, the city’s rift is providing momentum for environmentalists advocating for the rivers. By putting the Public Utilities Commission in the spotlight, they hope to see more of a backlash, and in doing so weaken the hand of San Francisco, which they view as a major hurdle to the state’s effort to rescue the river system.

“The SFPUC is not representing the values of its residents,” said Peter Drekmeier, policy director of the Tuolumne River Trust. “We expect the Central Valley irrigation districts to oppose the plan. But San Francisco?”

“And, yes, (the city has) a lot of influence over this,” he said.

At issue is how much water should flow from the Sierra Nevada’s many rivers to the Sacramento-San Joaquin River Delta, a vital ecological and water-supply hub where the state’s two largest waterways converge. As it stands, most of the rivers feeding the delta run at only a fraction of their natural flow because of the heavy draws by cities and farms.

The result has been declining water quality and lost wildlife habitat. The chinook salmon population is collapsing, a blow that has reverberated up the food chain to eagles, orcas and beyond. The delta estuary is menaced with invasive weeds and pollution.

Under the plan, the State Water Resources Control Board is proposing that no more than 60 percent of the flows of the San Joaquin River and its tributaries, on average, be taken from the channels during certain months in the winter and spring. The average flow now is less than 30 percent. A similar proposal is forthcoming for the Sacramento River.

State officials tout their effort, formally known as the Bay Delta Plan, as a compromise that will save the delta and the rivers while still leaving the bulk of the water for human consumption.

San Francisco and some of the state’s largest irrigation districts, however, contend they won’t get enough water to support their needs.

The Tuolumne River, the source of San Francisco’s famously pure Hetch Hetchy supply, averages just 21 percent of its historic flow at peak runoff. Meeting the state’s target would mean drawing 7 to 23 percent less water from the Tuolumne and other rivers in the San Joaquin River watershed, according to state estimates.

Officials at the Public Utilities Commission acknowledge that in wet years there wouldn’t be any supply problems. But when it gets dry, they say, residents and businesses would invariably face water rationing — as much as a 40 percent reduction during a severe drought. Over the long run, as new water sources are developed, water rates could increase, they say, up to 17 percent over 15 years.

Much of the hardship would extend to the roughly two dozen Bay Area communities that purchase water from the city.

Michael Carlin, deputy general manager for the Public Utilities Commission, said the city agency is not ignoring the health of the river. The utility invests millions on restoring the Tuolumne’s habitat. But Carlin said he has to look at more than just fish.

“I’m responsible for clean drinking water and protecting the environment, and there’s a cost to doing both,” he said. “It’s a balance sometimes. People don’t always see that balance. But it’s there.”

Officials at the Public Utilities Commission were not aware of any formal push by the Board of Supervisors to block their opposition to the state’s effort, saying only that they had been in conversation with board members about the matter.

“I don’t think we’re going to change course at this point,” Carlin said.

San Francisco has played an outsize role in the statewide debate over the Bay Delta Plan.

While water issues often split between agricultural and urban interests, the city’s resistance to the plan has created an unusually powerful bloc with the farming industry to take on the state.

“I’m totally amazed that the State Water Board has been able to stick to their guns,” said Heinrich Albert, a water committee co-chair at the San Francisco Bay chapter of the Sierra Club. Albert has fought for the state’s initiative but acknowledges the city’s power to derail it.

The city-farm alliance has recently won the backing of the Trump administration. Interior Secretary Ryan Zinke this summer criticized the Bay Delta Plan as being unfair to water users while President Trump has taken to Twitter to call the state “foolish” for not wanting to pump more water from rivers.

The latest show of support from Washington came as a subtle, yet surprising move by the Fish and Wildlife Service. This month, the agency shied away from what had been widely construed as an embrace of the Bay Delta Plan’s proposed flow increases. In a letter submitted to the Federal Energy Regulatory Commission on a separate but related issue of dams on the Tuolumne River, the agency said its strategy for protecting wildlife habitat could be accommodated with lower river flows.

A spokesman for Fish and Wildlife called the change in direction necessary “to balance the needs of people and nature.” But supporters of the restoration were quick to suspect that the shift was the result of pressure from above.

Talks between water users and the state, mediated by former Interior Secretary Bruce Babbitt among others, have been ongoing. But so far they’ve produced no meeting of the minds. The State Water Board is scheduled to vote to approve the proposed targets for the San Joaquin River watershed next month. The decision has already been postponed once because of the disagreement.

Research by the state and independent scientists has shown that boosting water levels is the only way to salvage California’s river system. A technical report by the State Water Board has recommended maintaining at least 60 percent of the natural flow of the San Joaquin River and its tributaries, though the board is willing to accept 40 percent for the sake of compromise.

The city’s Public Utilities Commission, meanwhile, has put forth alternative research, backed by the Turlock and Modesto irrigation districts, that suggests that the Tuolumne River can be restored without drastically cutting back on the amount of water taken out.

The study, performed by water agency scientists, calls for more habitat improvements, from planting trees along the river banks to enhancing gravel beds for fish to removing the invasive creatures that prey on salmon.

Critics have dismissed the city’s report as simply self-serving.

Supervisor Peskin said he hopes the Public Utilities Commission will eventually stand down, and he’s been speaking with agency officials to encourage them to do so. If they don’t, though, he believes he’s got a good shot at forcing their hand.

A resolution from the Board of Supervisors that proclaims the city in support of the Bay Delta Plan would not necessarily require the Public Utilities Commission to adopt the city’s position. The water agency operates independently of City Hall, with its own governing board, budget and staff.

However, the supervisors hold certain powers over the Public Utilities Commission. They must approve large infrastructure bonds and sign off on budgets, for example, and Peskin said he’d leverage that authority if the agency declines to cooperate.

“The bottom line is that if the Board of Supervisors were to set the policy of the city and county as having larger, unimpaired flows (in the river system), that would be a pretty significant move,” Peskin said. “It would have both political and legal implications.”

At least two of San Francisco’s 11 supervisors have expressed formal support for the Public Utilities Commission in letters to the state. But Peskin believes he could win enough votes from the others to pass a resolution.

Mayor London Breed, who would have veto power over the measure, declined to comment for this story.

The governing board of the Public Utilities Commission, which typically doesn’t get involved in the day-to-day affairs of the agency, like lobbying against the Bay Delta Plan, appears to be taking a greater interest in the issue. The board is nominated by the mayor and approved by the supervisors.

Board member Francesca Vietor told The Chronicle that she has reservations about her agency’s stand.

“As a San Francisco resident and a commissioner, I’m not willing to compromise the well-being of our fish, rivers and ecosystems,” she said. “I’m not convinced we can’t get to a better set of solutions.”

Commissioner Ike Kwon also expressed concern for the health of the rivers but appeared more confident in his agency’s ability to protect both wildlands and water supplies.

“In a sense we’re all environmentalists,” he said, “just to a different degree.”

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