LA GRANGE, Stanislaus County — The cold, rushing water of the Tuolumne River, piped from the high peaks of Yosemite to the taps of Bay Area residents, is not only among the nation’s most pristine municipal water sources but extraordinarily plentiful.

This point of pride for San Francisco, which has maintained rights to the cherished Sierra supply since the early 1900s, is being threatened, however. Under a far-reaching state plan to bump up flows in California’s rivers, the city would be forced to limit its draws from the Tuolumne for the first time in recent memory.

City leaders call the restrictions unthinkable. They fear unprecedented water cutbacks for Bay Area residents and even businesses, and they’ve forged a strange marriage with farm communities which worry the plan will leave crops with insufficient water. Together, they have asked the state to scale back its initiative, but the state hasn’t budged, and another front in California’s enduring water wars has opened.

The intent of the California Water Resources Control Board is to rescue the Sacramento-San Joaquin River Delta. The West Coast’s largest estuary and a vital water source for much of the state has become short on water and wildlife as thirsty cities and farms have squeezed the rivers that nourish the delta. The Tuolumne is one of those rivers.

Near La Grange (Stanislaus County), a foothill town miles downstream of where San Francisco and agricultural suppliers take their water, the Tuolumne shrivels to a crawl. The river here is warmer and murkier, too. Most of the salmon are gone. The oaks and cottonwoods that offer shade and sustenance to animals along the riverbanks have thinned. Wildlife-viewing signs on the road over-promise.

On a recent afternoon, a group of kayakers had just enough water to paddle around a shallow bend in the river while a family of four waded in a knee-deep pool.

“We recognize that we’re not going to have flows like there once were,” said Patrick Koepele, an avid rafter and executive director of the Tuolumne River Trust, which has been pressing the state to salvage the lower reaches of the river. “But we want more flows than we’re getting now.”

The state’s restoration plan, which will be discussed by the State Water Board this week, calls for restricting water draws from the 149-mile-long Tuolumne and two other major tributaries of the San Joaquin River: the Stanislaus and Merced.

The board is expected to address flows on the larger Sacramento River and its tributaries in coming months. The hope is that higher river levels across California will increase inflow to the delta and rejuvenate the declining ecological and water-supply hub.

The central question of debate is whether the state’s push for the environment has gone too far, threatening commerce not only in California’s farm belt, but also in its urban centers where the growth of tech, housing and retail is on the line.

Between 7 and 23 percent less river water on average would be available for human consumption, and sometimes more, according to state estimates.

“The concern is that this would hit commercial and industrial customers,” said Steve Ritchie, assistant general manager for water for the San Francisco Public Utilities Commission, which provides water to the city, the Peninsula and South Bay.

While the plan would have little bearing on how much water Bay Area communities get during wet years when there’s plenty to go around, periods of drought would force the utility’s customers to go beyond making cuts to landscape irrigation. It would cause them to sacrifice water use in their homes and offices, Ritchie said.

A prolonged dry spell like the one between 1987 and 1992, according to agency projections, would force cuts of up to 40 percent, which Ritchie said is simply unsustainable for a thriving metropolitan area that already conserves more water than most.

The large and unlikely alliance of San Francisco and several big agricultural suppliers has recently won support from the Trump administration.

Interior Secretary Ryan Zinke threatened last month to intervene to hobble the state’s plan, and President Trump recently weighed in with a tweet, accusing California of “foolishly” leaving water in the rivers and not sending it to such spots as farms.

State officials acknowledge the plan will cause a drop in farm production — an average of 2.5 percent annually — in the region irrigated by the rivers, where lots of alfalfa, almonds and peaches are grown. Local leaders expect a bigger hit.

“Our whole economy is predicated on agriculture,” said Vito Chiesa, a walnut grower and Stanislaus County supervisor. “You take away our one strong suit, and you’ve sent us into a downward spiral (that) I don’t know how we get out of.”

The state’s plan, sometimes called the Bay-Delta Plan, aims to forge a middle ground between water users and wildlife.

It demands that 40 percent of the natural flow of the Tuolumne, Merced and Stanislaus rivers remain in the waterways — leaving 60 percent available to cities and farms — during the critical February-to-June period. This is when snowmelt provides a healthy flush for the river basins and helps juvenile chinook salmon make their way to the Pacific Ocean.

As it stands, the rivers run at only a fraction of their natural levels.

The Tuolumne River, which is constrained by five major dams, including San Francisco’s flagship Hetch Hetchy Reservoir in Yosemite National Park, averages only 21 percent of its historic flow between February and June, according to the state. It often contains less water.

Salmon numbers are down in the Tuolumne. Just hundreds of the imperiled fall-run fish have spawned in recent years, compared with tens of thousands a few decades ago. The fish serve as an indicator of the river’s health, and their populations help sustain other animals, from eagles in the High Sierra to orcas at sea.

Conservationists and fishing groups have asked the state to go even further to help the delta, calling for at least half of the water in the rivers to remain there. The advocates cite studies by the California Department of Fish and Wildlife and independent scientists suggesting that anything less will do little to improve the ecosystems.

“Fish and wildlife that depend on these rivers are getting short-changed,” said Doug Obegi, a senior attorney at the Natural Resources Defense Council. “This isn’t just a water supply. These are places. These are rivers.”

Both sides have threatened to sue the state if things don’t shake out the way they want them to.

In the face of division, the State Water Board last week postponed this week’s scheduled vote on the first phase of the plan at the request of Gov. Jerry Brown’s secretary of natural resources. The board will instead listen to public comment without taking action.

Secretary John Laird said in an email that he is holding out hope for a compromise.

But the warring parties remain a long way apart. The San Francisco Public Utilities Commission, with support from the Central Valley’s powerful Turlock and Modesto irrigation districts, is standing by an alternative strategy it pitched last year for restoring the delta.

That plan proposes rehabbing portions of the Tuolumne River to accommodate salmon and other wildlife, including enhancement of gravel beds and planting trees along the shoreline — not simply raising river flows.

“We agree that you need to put more water down the river, but you have to do it in an efficient way,” Ritchie said, noting city-sponsored studies that suggest timed water releases instead of constant discharges can help fish migrations.

Also, the San Francisco Public Utilities Commission has rejected suggestions that it could replace river water with alternative supplies, either purchasing them from other agencies or building a desalination plant. Officials cite low water availability and high cost as obstacles.

Conservation groups, though, continue to question the city’s commitment to restoring the state’s river system.

Jon Rosenfield, lead scientist for the Bay Institute, which works to defend the waters between the Sierra and San Francisco Bay, said city officials have used bad science and excuses to justify business as usual.

“San Francisco is seen as the capital of environmentalism, and the city’s ratepayers are being represented by an agency that says, ‘We’re not going to protect the environment,’” he said.

“We have an opportunity to fix this now. We have a once-in-a-generation opportunity. We need to act.”

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