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Flooded farm fields provide habitat for migratory water fowl on Staten Island in the Sacramento-San Joaquin River Delta near Walnut Grove on Jan. 6, 2020. Delta farmers are among those being told not to draw water amid a third year of drought.

Old River runs through farmland in the Sacramento-San Joaquin Delta outside Discovery Bay, Calif., on Tuesday, December 11, 2018. On Wednesday, the Legislature is expected to vote on a massive water bill which could decide the fate of the state's water, pitting environmentalists and sportsmen against farmers and city dwellers. No matter how the vote goes, someone will be unhappy, either the cities and suburbs, or the ranchers/farmers or the environmentalists.

Emilio Alcantar, 49, uses suction to pull water into a tube as part of the furrow irrigation process for 90 acres of tomatoes on Bowles Farming Co. land July 24, 2014 in Los Banos, Calif. Cannon Michael, the president of the company, is concerned about sinking ground in a nearby area, which is making it harder for the groundwater under his land to get to it as the angle increases below the surface. Most Central Valley farmers received no more than a 5 percent water allotment this season from government water sources, leaving many farmers with no choice but to pump ground water to keep their businesses afloat. The San Luis Canal Company is a private water company that sells to nearly 100 farmers working 45,000 acres in the Los Banos area. The company has historic water rights allowing it to ship water from the San Joaquin River even in dry years, and it also supplements its supply with a small amount of ground water. Over the past few years, though, Chase Hurley, General Manager of the San Luis Canal Company, has been concerned about the long-term effects of heavy ground water pumping from nearby land. Hurley and others have found that the ground in certain areas is sinking half to a quarter of a foot a year because of the pumping. The sinking ground has brought up concerns with possible flooding into nearby farmland from a dirt canal designed for routing flood water past the area. Hurley is also concerned that the company's dam will begin losing water as the land continues to sink. Farmers in the area are working together to try and curb the problem themselves by replenishing the aquifer. One of the plans involves leaving specific acres of land inactive with the intention of using it to capture water when it does rain again, says Hurley. Local farmers stand to lose business if the ground water supply declines, and...

In one of the most far-reaching efforts to protect California’s water supplies this year, state regulators on Tuesday ordered thousands of farmers, irrigation districts and municipal water agencies, including the city of San Francisco, to stop making draws from rivers and creeks.

The move, which comes amid a third year of the California drought, forces water users, from individual landowners to utilities serving tens of thousands of people, to turn to alternative sources of water, if they have it. Some growers and small water providers without a backup supply may be forced to go without water entirely.

The action marks an unusually extensive application of the state’s water rights system, a policy that reserves California’s limited flows for those with the most senior claims to water. Officials with the powerful State Water Resources Control Board said they needed to push in to the system because there’s simply no longer water for everyone. Erik Ekdahl, deputy director of the agency’s Division of Water Rights, called the restrictions — known as curtailment orders — “significant” and “very deep.”

The orders, effective Wednesday, apply to those with lesser water rights in the sprawling Sacramento and San Joaquin river watersheds, basically inland areas from the Oregon border to Fresno. The extent of the water rights affected varies by location, but state records show that a total of 4,252 rights will be curtailed, including those of 212 public water systems.

For the large public agencies, including the San Francisco Public Utilities Commission, which provides water to San Francisco and several suburban communities in the Bay Area, the curtailment means leaning on groundwater, waterways that are not restricted or water held in storage.

Although the curtailments prevent water in rivers and creeks from being diverted into reservoirs, water that’s already in storage, which is a primary source of water for the big utilities, is not affected. The SFPUC maintains water in several reservoirs in and around Yosemite National Park, most of which are now near full.

Officials with the SFPUC had not yet received their orders from the state water board as of Tuesday afternoon. They declined to comment until they had.

While the curtailments may have little immediate impact on the city’s water supply, San Francisco officials have been critical of past efforts to limit water rights, specifically rights from 1914 and older, which are considered senior. Many senior rights holders don’t think the state has authority to restrict such claims and don’t want to see the state set a precedent of curtailing them. Three of San Francisco’s pre-1914 water rights, all along the Tuolumne River, are affected by the new orders.

The biggest toll of the curtailment will be on farmers, particularly those in the San Joaquin Valley, the state’s agricultural heartland. Only a small number of water rights holders are being restricted in the Sacramento Valley, to the north, whereas in the San Joaquin Valley, some with water rights dating back to 1900 are cut off.

Chris Scheuring, water attorney for the California Farm Bureau Federation and whose family grows tree crops in Yolo County, said Tuesday’s orders inevitably mean an aggregate drop in farm income, farm employment and the availability of fruits, vegetables and nuts in grocery stores.

“Californians will ultimately have less California produce because of this,” he said. “Obviously curtailments never go down easy. Water is the lifeblood of farming.”

The new curtailment orders don’t quite reach the level of last year’s, but they come two months earlier than the enforcement of last year’s restrictions, at a time when many water users, particularly growers, are heavily dependent on spring runoff. Additionally, water regulators can broaden the reach of this year’s limits if need be.

Still, the breadth of the new curtailments is not common. The state water board often restricts some junior water rights holders in areas when water is low, but rarely are the orders as geographically sweeping and go as far down the hierarchy of water rights.

The curtailments cease only when regulators deem there to be sufficient water for all rights holders, as was the case last year after rains began in the fall. Consecutive years of restrictions, though, can impose a cumulative burden.

A handful of other areas have been subject to curtailment orders this year, or are expected to, though not to the same extent as in the Sacramento and San Joaquin river watersheds. On Tuesday, the state water board also approved a novel plan that allows water right holders in the upper Russian River watershed to voluntarily reduce water use in lieu of having their diversions curtailed.

California’s water rights have been acquired, for more than 150 years, on a first come, first served basis. Landowners with property along rivers and creeks also have preference. How the water is used is not a factor in determining who gets cut off first, though if human health and safety are impacted, the water rights holder can petition for an exemption. Anyone taking water from a river or creek, whether a single homeowner, a farming operation or a city, must have a water right.

The curtailment orders are among a number of tools that the state has used during the current drought to conserve water. The state water board recently enacted regulation that requires municipal suppliers across California to prepare for water shortages of up to 20% while the state Department of Water Resources has been severely limiting deliveries from state-managed reservoirs.

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

Kurtis Alexander is an enterprise reporter for The San Francisco Chronicle, with a focus on natural resources and the environment. He frequently writes about water, wildfire, climate and the American West. His recent work has examined the impacts of drought, threats to public lands and wildlife, and the nation's widening rural-urban divide.

Before joining the Chronicle, Alexander worked as a freelance writer and as a staff reporter for several media organizations, including The Fresno Bee and Bay Area News Group, writing about government, politics and the environment.