WILLOWS, Calif. — When the winter rains failed to arrive in this Sacramento Valley town for the third straight year, farmers tightened their belts and looked to the reservoirs in the nearby hills to keep them in water through the growing season.

When those faltered, some switched on their well pumps, drawing up thousands of gallons from underground aquifers to prevent their walnut trees and alfalfa crops from drying up. Until the wells, too, began to fail.

Now, across California’s vital agricultural belt, nervousness over the state’s epic drought has given way to alarm. Streams and lakes have long since shriveled up in many parts of the state, and now the aquifers — always a backup source during the region’s periodic droughts — are being pumped away at rates that scientists say are both historic and unsustainable.

One state-owned well near Sacramento registered an astonishing 100-foot drop in three months as the water table, strained by new demand from farmers, homeowners and municipalities, sank to a record low. Other wells have simply dried up, in such numbers that local drilling companies are reporting backlogs of six to eight months to dig a new one.

In still other areas, aquifers are emptying so quickly that the land itself is subsiding, like cereal in a bowl after the milk has drained out.

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California’s record drought brought very little snowpack this past winter, placing extra demands on the state’s aquifers.

“How many straws can you stick into one glass?” asked John Viegas, a county supervisor who, after months of fielding complaints from constituents about water shortages, recently was forced to lower his own well by 40 feet. “People need to realize you can’t water everything.”

The shrinking of the aquifers has added a new dimension to the concerns over the historic drought that continues to shatter records across the Western United States. The parched zone now spans a dozen states and nearly 600 counties, from southern Texas to the northern Rockies, and includes fields and grazing land that produce a third of the country’s beef cattle and half of its fruit, vegetables and winter wheat. Prices for most of these products have soared this year.

Hardest hit is California. As of last month, nearly 60 percent of the state is officially in an “exceptional” drought — the highest level, above “severe” — and meteorologists are seeing no immediate change in a relentlessly dry forecast. Indeed, scientists are warning that the state’s cyclical droughts could become longer and more frequent as the climate warms.

If that happens, the elaborate infrastructure built to deliver water to the state’s 38 million residents and 27 million cultivated acres may not survive the challenge, new research suggests. Already the drought has led to the “greatest water loss ever seen in California agriculture,” said a study last month by researchers at the University of California at Davis.

A massive shift to groundwater helped farmers survive this year, but if pumping continues at current rates, some of the state’s aquifers could soon be depleted, the study warned. One of the authors, Richard Howitt, a professor emeritus of resource economics, likened the problem to a “slow-moving train wreck.”

“A well-managed basin is used like a reserve bank account,” Howitt said. “We’re acting like the super rich who have so much money they don’t need to balance their checkbook.”

The study estimated that 5.1 million acre-feet of water will be pulled from the state’s underground reserves this year, a volume roughly equivalent to the storage capacity of Lake Shasta, the state’s biggest reservoir and third-largest lake after Lake Tahoe and the Salton Sea.

Joe Carrancho has had to fallow 25% of his rice acreage due to a lack of water. (Max Whittaker/Prime/For The Washington Post)

Damage to aquifers is viewed as more serious because, once depleted, an aquifer takes far longer to replenish — often decades or more, compared with a few years for an empty reservoir, said Thomas Harter, a groundwater specialist from the university’s Land, Air and Water Resources Department.

“It’s a downward path,” he said. “We cannot do what we did this year on a permanent basis.”

Droughts in California are hardly new. Big ones come around every decade or two, the Western equivalent of the super-hurricanes that occasionally strike the East. The archeological record points to far worse droughts in the distant past, including some that lasted more than 50 years.

But that was before millions of people lived along the coastal bays, and before the state’s great Central Valley sprouted one of the most productive agricultural districts in the history of the planet.

Still, the current drought is the worst in California’s recorded history, and some of the costs are as visible as the retreating shorelines and bone-dry marinas of the state’s fresh-water lakes. Dozens of California cities and towns have imposed tough restrictions on water use, and many have posted fines of up to $500 a day on violators. In the state’s parched woodlands, fire crews chased 140 new wildfires in just the past week.

Large cities such as Los Angeles have coped with the water shortage by drawing from dedicated reservoirs constructed after previous dry spells, part of a celebrated “drought-proofing” effort promoted by politicians and urban planners. But those stores of water could also be threatened if the drought continues, scientists say. State officials have had to scramble to find drinking water for smaller towns and villages where supplies have all but run out.

In the state’s farm belt, the drought’s effects are less obvious, obscured by miles of still-lush walnut orchards and vast rice plantations where the knee-high green stalks mature in shallow pools of brown water. But the damage has been severe here, too. Some of it is visible in dry irrigation ditches and barren fields belonging to farmers who received no water allotment this year. Other wounds are hidden, such as aquifers that became contaminated with salt or farm chemicals after months of overpumping, or household wells that now pull up nothing but air.

It was never supposed to get this bad. For decades, the Central Valley’s farmers relied on their own form of drought-proofing: a vast network of reservoirs and irrigation canals built over decades to capture annual snow melt from the Sierra Nevada mountains. And to recoup the costs of expensive irrigation systems, they switched to more profitable crops such as almonds, walnuts and rice, which require still more water.

But no one counted on having consecutive seasons in which the mountain snows never arrived. This year, the high peaks have been all but bare, causing the already depleted reservoirs to drop further. What was left in the canals had to be divvied up among thousands of farmers based on a complex seniority ranking, with large quantities set aside by law to ensure the survival of natural wetlands and salmon fisheries downstream.

Jeffrey Sutton, who supervises 140 miles of irrigation channels in the western Sacramento Valley for the Tehama Colusa Canal Authority, warned his customers to expect less water this year. It was even worse than he feared: While some farmers ended up with 75 percent of their usual allotment, many others received nothing at all.

“This was the first year it ever went to zero,” Sutton said from an office overlooking the network’s cement-lined main channel. “You can’t allocate water that’s not there.”

Some farmers could afford to cut back on spring planting, but those with permanent crops — peach orchards and almond trees that pay off slowly after years of investment — had to scramble to find alternate supplies. Some others paid hefty fees to buy water rights from their neighbors, while others joined the race to drill, installing new wells at a cost of thousands of dollars each.

For Sutton, whose family has farmed the region for three generations, any outing to church or the local store was apt to include an awkward exchange with a neighbor worried about what could happen if the drought lingers for a fourth year.

“It is unparalleled crisis, unlike anything we’ve experienced,” he said. “People are emotional. There’s a fear of losing farms that have been passed through families for generations.”

For Willows, Calif., farmer Joe Carrancho, the immediate worry is how long he can continue paying his 14 employees, men who have tended his rice farm for years and are “damn-near family,” he says. Carrancho, 71, is regarded as one of the luckier ones, having lost only 25 percent of his usual water allotment this year. Still, with a quarter of his fields now idle, he says he will have to stretch to make payroll while keeping up payments on the $500,000 rice harvester sitting in his barn.

“I’d much rather be growing rice here,” said Carrancho, kicking up dust in an empty field of pecan-colored earth beside his modest ranch house. “I have 25 percent less production, but no one is giving me a 25 percent break in my bills.”

In the state capital, worries over the shrinking water supply have kindled fresh conflicts along the state’s traditional fault lines: rural and urban, environmentalist and property owner, Republican and Democrat. Opposing factions have clashed repeatedly in recent weeks over how the government should address current and future water shortages.

On Wednesday, state lawmakers passed a $7.5 billion bond measure that, if approved by voters this fall, would expand the state’s reservoirs and improve water recycling and other conservation measures. Two separate measures undergoing debate would impose the most significant restrictions on groundwater use in California history.

Farming groups say they are open to compromise, though many in their ranks are scornful of any talk of regulating water that lies under private lands. Many farmers also insist that government agencies helped instigate the current crisis, both by mandating the diversion of millions of gallons of water for environment uses, and by allowing runaway urban development in the some of the state’s driest regions.

Yet, agriculture’s huge appetite for water makes it an easy target for state officials looking for ways to conserve. Irrigation accounts for 41 percent of the state’s water use, compared with 9 percent for urban water systems. And the recent shift to crops such as alfalfa and rice has prompted questions about whether this drought-prone region is suited for water-intensive agriculture.

“We’ve reached a tipping point where the surface water is no longer enough, yet there are increasing demands from both agriculture and the environment,” said hydrologist Graham Fogg, a groundwater management expert.

A short-term solution, strongly favored by growers and some elected officials, is to increase the state’s water storage capacity, either with new or expanded reservoirs or dedicated aquifers underground. Farmers say extra storage will allow them to meet their needs even if droughts become more frequent.

“Our best storage is those mountains,” said organic rice grower Bryce Lundberg, gesturing to the normally snowcapped Sierra Nevada peaks, visible from his fields in Richvale, Calif. “When you see snow up there, the mountains are essentially holding water for California. But if climate change is happening, we need to invest in storage, because if we’re not seeing white mountains, we need to see blue water.”

But environmentalists and many scientists argue that any long-term solution would have to balance competing interests, including the need for clean water for growing cities as well as thriving habitats for fish and wildlife. A recent modeling study by researchers at UC Davis’s Center for Watershed Sciences suggested that California’s economy could weather far more severe water shortages — and even a decades-long drought similar to the ones that occurred millennia ago. But doing so would require not only more storage for water but also a general willingness by all sides to make do with less.

“Keeping the balance may mean reducing the number of irrigated acres, but if you manage the system well you can still do amazing things with it,” saidJay Lund, a professor of civil and environmental engineering who participated in the exercise. Lund said he believes Californians are more capable of adjusting, compared with people in other water-challenged parts of the world, because they already possess experience and expertise and “because we happen to be rich, which helps.”

Despite his engineer’s optimism, Lund keeps a prayer of sorts taped to his office door. It is a two-word play on the University of California’s motto, “Fiat Lux,” or, in Latin, “let there be light.”

“Fiat Pluvia,” Lund’s sign reads.

Let there be rain.