The San Francisco Board of Supervisors issued a rare rebuke of the city water department Tuesday, claiming the agency is on the wrong side of a state water debate that pits California against President Trump.

The San Francisco Public Utilities Commission, which provides water to the city and more than two dozen suburbs, has fiercely opposed a far-reaching state plan to revive California’s river system, including the languishing Sacramento-San Joaquin River Delta, because it means giving up precious water supplies.

The agency’s bid to protect its stake on the Tuolumne River, high in the mountains of Yosemite, and prevent potential water shortages has aligned it with similarly concerned Central Valley agricultural suppliers and their allies in the Trump administration. The unlikely alliance has created a powerful bloc that has so far succeeded in sidelining the state’s restoration effort.

San Francisco Supervisor Aaron Peskin put forward a resolution Tuesday, insisting that a city known for its environmental bona fides should stand up for the rivers and not partner with Washington to let them run dry. The board unanimously approved his measure, which pledges full city support for the state plan. The plan is scheduled to be taken up by state officials next week.

“It’s time for a new page,” Peskin said. “It is time not to act like a business enterprise, but realize the health of our region is at stake.”

The mostly symbolic resolution stops short of telling the quasi-independent Public Utilities Commission what to do. But it sends a signal to the water agency about where the supervisors stand and that more severe action could follow.

Officials at the Public Utilities Commission said after Tuesday’s vote that they had no intent to stop pushing for a solution that would provide more water to the city than is currently promised in the state proposal. They cited a provision in the resolution that allows for additional talks with the state.

“We support the goals of the state plan, but not the methods that they are using to get to that goal,” said spokesman Tyler Gamble. “We’re going to continue moving forward with the negotiations.”

Peskin has threatened to use the board’s budgetary powers to weaken the Public Utilities Commission if the agency puts up too much of a fight.

The initiative by the State Water Resources Control Board comes as the rivers that once poured from the Sierra Nevada run low because of relentless pumping by cities and farms. The lack of water has decimated the delta, a critical juncture for salmon and other wildlife as well as the hub of California’s water supplies.

To address the impending crisis, state officials want to boost the amount of water in the San Joaquin River and its tributaries that flow to the delta by limiting draws to no more than 60 percent of a river's flow during peak runoff periods. Currently, some rivers run at just 10 percent of their natural level.

The state water board is slated to vote on the proposal next Wednesday. A similar initiative for the Sacramento River and its tributaries is expected to follow.

Environmental groups and the fishing industry, which have long supported the state’s restoration effort, applauded Tuesday’s action by the Board of Supervisors.

“We have renewed hope that we’ll finally get a little bit more water in the rivers that is so desperately needed,” said John McManus, president of the Golden Gate Salmon Association.

Largely due to insufficient river flows, the number of salmon in the San Joaquin River watershed has plummeted to a fraction of the tens of thousands that spawned there just decades ago. The decline has had a heavy toll on fishermen.

McManus speculated that without San Francisco’s opposition, the state water board would be more inclined to move forward with its plan next week.

The Public Utilities Commission’s unlikely alliance with agricultural water suppliers on an issue often split between urban and rural interests had given city water officials unusual clout on the matter.

For more than a year, moderators tapped by the state to work with opponents of the state plan, including former Interior Secretary Bruce Babbitt, had urged the city to back off. So had Gov. Jerry Brown.

Peskin acknowledged that the Public Utilities Commission could continue to work behind the scenes to fight the state, but he said his resolution is almost certain to prevent the agency from taking legal action.

While state officials have touted the so-called Bay Delta Plan as a compromise that will help rescue California’s river system yet still leave the bulk of water for humans, several municipal water agencies and irrigation districts believe they’re not getting enough.

Meeting the state’s target on the San Joaquin River and its tributaries would mean drawing 7 to 23 percent less water, according to state estimates.

The San Francisco Public Utilities Commission has said the plan would necessitate immediate development of alternative water sources, like desalination plants, prompting higher water rates of as much as 17 percent over 15 years in order to fund the new infrastructure.

Water rationing may also be needed until additional supplies come on line, according to the agency.

“Our core responsibility is to deliver clean, reliable, safe drinking water,” said Harlan Kelly, the Public Utilities Commission general manager, at a committee hearing Monday on Peskin’s resolution. “We are prepared to put more aside, but we thought it must be done in a responsible way.”

The agency has maintained that it can revive struggling salmon runs on the Tuolumne River without major water cuts to cities, though the state and independent scientists say that’s not possible.

Opponents of the Bay Delta Plan have won recent support from Washington, where Interior Secretary Ryan Zinke has characterized the state’s proposal as a water grab and threatened to take legal action to stop it.

President Trump has criticized California on Twitter for being “foolish” for not wanting to pump more water from the rivers.

At Monday’s preliminary hearing on the San Francisco resolution, a handful of labor activists and workforce development officials also questioned the state’s push to withhold supplies from people when shortages could affect businesses and jobs.

Mayor London Breed has been mum on the issue. She declined repeated attempts by The Chronicle to get her to comment on efforts to restore the rivers and the delta ecosystem.

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