Most signs of California’s unrelenting drought are easy to spot, with mountaintops that should be snow-peaked this time of year stained brown and reservoirs in the heart of the state already half-empty.

But the most alarming feature of the state’s water shortage remains hidden from view, scientists say. California is running low on groundwater, the vast pools of water stored in underground aquifers that took thousands of years to fill up but are now being drained to irrigate farm fields and run sink taps.

Groundwater usage has surged as the state’s drought has dragged on, jumping to an estimated 65 percent of the fresh water used in 2014, from under 40 percent in normal years. This year, that number could hit 75 percent.

With summer’s baking heat still to come, and with projections by NASA scientists that water reservoirs could run dry, groundwater could account for virtually all of California’s water by year’s end, said Jay Famiglietti, a NASA senior water scientist who uses satellites to study the problem.

“It’s more scary than people realize,” Famiglietti said.

California Gov. Jerry Brown and top lawmakers announced a $1 billion emergency legislative package to deal with the state’s record-breaking drought. (Reuters)

Already, the state is showing signs of groundwater exhaustion. The water table is dropping two feet a year in parts of the thirsty, agricultural Central Valley. Even urban water utilities have noticed declines. Wells are running dry. Farmers are forced to dig deeper in the search for water.

And as the water is pumped up, the ground sinks down. In some places, the pace of subsidence could reach one inch a month for the rest of the year, said Thomas Harter, a groundwater hydrologist with the University of California at Davis. That could end up further damaging infrastructure, such as the state’s vital network of water canals.

The state’s water woes have been compounded by the four-year drought. The state’s reservoir system should be able to supply the vast majority of California’s water needs, if there is enough rain and snow. But with scarce precipitation, reservoirs are running short. That’s led to a heavier reliance on groundwater, said Famiglietti. He compared the state’s water system to different types of bank accounts.

Reservoirs can be refilled with runoff and downpours, like a checking account. But recharging underground aquifers — considered a savings account — is much more difficult.

“It’s the groundwater that is the really big, important account,” Famiglietti said.

The current predicament has been exacerbated by decades of allowing groundwater usage to be essentially unmanaged — a case of “out of sight, out of mind.” Regulations were few. Almost anyone could drill down and tap into a stressed aquifer.

Last year, state lawmakers passed California’s first extensive groundwater regulation, allowing for the creation of local boards to oversee how the water is used. But it could be two decades before the new law takes full effect.

Amid an historic drought, Californians are preparing to face the reality of their first statewide mandatory water restrictions. (Reuters)

The Central Valley has experienced the worst effects of the groundwater problem. The aquifer tucked beneath farm fields stretches for 400 miles, making it the state’s largest water reservoir. Today, more than 100,000 wells have stuck straws into the reservoir. More than 15 percent of all the groundwater pumped in the United States comes from this one resource, said Claudia Faunt, a hydrologist with the U.S. Geological Survey.

Faunt has seen how water use has changed in the Central Valley. Farmers have planted more water-intensive, high-profit crops, with pistachios and almonds needing extensive watering. At the same time, housing developments have encroached on arid farm fields. Underground reservoirs are no longer an emergency resource.

“They’re pumping groundwater even in years when there is no drought,” Faunt said.

The result, Harter said, is that the state’s groundwater reached historic lows last year.

“With little recharge, many areas are currently at the lowest recorded levels ever,” Harter said. “It’s worrisome.”

California’s water shortage has hit Andy’s Orchard, a 60-acre spread of cherry, apricot and peach trees outside San Jose.

For years, the orchard used surface water drawn from the San Luis Reservoir to water its trees. Last summer, water officials closed the tap as farmers across the state saw their water allotments slashed.

Owner Andy Mariani was left scrambling. He finally struck a deal with a neighboring farmer who pumped from a groundwater well. Since then, Mariani has been buying water from his neighbor.

He’d prefer to be using reservoir water. But he’ll take what he can get.

Recently, Mariani learned his neighbor would be planting peppers soon. He could supply Andy’s Orchard with groundwater for only two more weeks.

“We don’t know where the next drop of water is coming from,” Mariani said.