As California heads into its annual rainy season, water managers, farmers and millions of residents with parched yards are hoping huge storms will finally break the state’s historic three-year drought.

Don’t count on it.

It may be raining this week, but unless near-record rain falls between now and next spring, it’s likely the drought will continue through 2015, experts say. That’s because California has so much catching up to do — from near-empty reservoirs to depleted wells to parched rivers.

An analysis of National Weather Service records shows that many of the state’s major cities have received so little rain in the past three years that their “rainfall deficit” heading into this winter is actually larger than the rainfall total they receive in an average — or even record — winter. And in some cases the past three years have been the driest three-year period in recorded history.

“The bottom line is that it is going to take a pretty exceptional rainfall year to get us back out of the hole in one year,” said meteorologist Jan Null, owner of Golden Gate Weather Services in Saratoga.

Null, who worked at the National Weather Service for a quarter century and who analyzed the data with this newspaper, compares the state’s plight to a family’s severe financial troubles, which usually take years to resolve.

“It’s like having a lot of credit card debt,” he said. “We have a big deficit.”

San Jose, for example, received 22.83 inches of rain from July 1, 2011 to June 30, 2014. That’s the driest three-year period in 125 years. In an average three-year period, the city receives 42.9 inches — a shortfall of 20.07 inches.

The city would not only have to make up that amount just to get back to even, it would also need another normal year’s total of about 14 inches this winter to have an average 2014-15.

That’s roughly 34 inches. But even during the wettest winter in San Jose history, 1889-90, it rained less than 30.3 inches.

Similarly, San Francisco begins the winter 18 inches short of its average three-year total. Oakland is 24 inches behind. Los Angeles is 23 inches behind. And Fresno is nearly 12 inches behind.

Conserving

Managers across the state are worried that after the first storms arrive, many Californians will assume the drought is over and stop conserving.

“It is a real concern,” said John Coleman, a board member with the East Bay Municipal Utility District, which supplies water to 1.3 million people in Alameda and Contra Costa counties. “You should not revert back to what your usage was because of a few storms. We don’t know how the rest of the year is going to play out.”

Even with modest recent storms, Bay Area rainfall totals are already below average levels for this rainy season. Worse, the National Oceanic and Atmospheric Administration announced last week that the chances of El Niño conditions this winter — which can increase the chance of rain — are now only 58 percent, down from 82 percent in June.

To be sure, water experts note that every single “lost inch” of rain since 2011 doesn’t have to be made up for the drought to be over.

“The way you know you are out of a drought is because the reservoirs are all spilling,” said Jay Lund, a UC Davis professor of civil and environmental engineering.

They are far from that point.

Reservoirs

Shasta Lake, the largest reservoir in California, is 24 percent full. Similarly, Lake Oroville in Butte County, the second-largest reservoir in the state, is 26 percent of capacity. San Luis Reservoir, along Highway 152 in Merced County, is just 20 percent full.

All 10 reservoirs in Santa Clara County are only 30 percent full combined. And several, like Chesbro, Uvas and Guadalupe, are below 5 percent — essentially empty.

The streams and rivers that fill those and thousands of other lakes are near historic low flows.

“With a moderately good rain year, the streams will start flowing,” Lund said. “It will take more than an average year to fill up the reservoirs. And it will take a really, really wet year to fill up the aquifers.”

With little rainfall, a small Sierra snowpack and low flows in rivers since 2011, many cities and farm areas have been relentlessly pumping groundwater to make up the difference.

In Santa Clara County, the groundwater is now at the lowest level in 25 years, said Marty Grimes, spokesman for the Santa Clara Valley Water District, adding that the water table under San Jose has fallen 65 feet since 2011.

“We fully expect our call for conservation continuing well into 2015,” he said.

All year, the district has asked the public to cut water use by 20 percent. In September, Santa Clara County cut water use by 14 percent compared with the previous September. Similarly, EBMUD customers cut use by 13 percent, while San Francisco cut 9 percent, Contra Costa County cut 21 percent, Los Angeles cut 8 percent and San Diego cut 3 percent.

Fearful of lost water sales and political backlash, few California cities have decided to issue fines for overuse of water or set water budgets for homeowners this year. But there’s little doubt that strict rationing — coupled with big fines — works. Santa Cruz, which enacted those measures last spring, cut water use 30 percent in September compared to September 2013.

Leniency could be a thing of the past, however, if California has another dry winter.

“We’ll be looking at everything,” said Coleman of EBMUD. “It’s a whole new game.”

That could include fines for overuse, a ban on all outdoor watering and other tough measures, he said.

Groundwater depletion is an even bigger problem in the Central Valley. There, in each of the last three years, farmers have pumped out about 6 million acre feet of water from the ground — triple the amount of a normal year, said Jay Famiglietti, a senior water scientist with NASA’s Jet Propulsion Laboratory in Pasadena.

It will take decades, if ever, to get it back, he said.

“The hole that nature has dug and we have made deeper because of our groundwater use is so big, even one big winter is not going to do it,” he said. “The reservoirs are way too low, and the groundwater is way too low. It will have to rain and rain and rain.”

Paul Rogers covers resources and environmental issues. Contact him at 408-920-5045. Follow him at Twitter.com/PaulRogersSJMN