Groundwater—water from underground wells pumped to the surface—will likely offset more than 70 percent of the lost surface water (water obtained from snow, rain and irrigation) researchers noted.
Water users will draw 67 percent more groundwater this year than they did in 2014, and they will spend 30 percent more money doing it.
That alone will cost nearly $600 million, and could have far-reaching effects on the state's future groundwater supply, which is a crucial source of water during dry periods.
Read MoreCalifornia landowners resist efforts to monitor groundwater
Researchers say groundwater use still isn't monitored closely enough, and they're concerned that overdrawing may make it difficult to replenish, or have other unexpected effects, such as creating long-term geological changes.
In the meantime, using groundwater is the equivalent of living on credit, said Richard Howitt, a professor emeritus of agricultural and resource economics at UC Davis.
"The impact is nowhere near what you would expect because of groundwater, which is covering most of the surface water lost," Howitt told CNBC. "What I would say is it is like someone who got laid off living off of a good line on a credit card. You have something to fall back on, but you are racking up debt."
Improved understanding of the state's groundwater supply will let researchers better determine when—and how far—levels will drop, Howitt said.
Furthermore, groundwater supplies are not evenly distributed across the state's agricultural regions. Double-digit unemployment is already afflicting farming towns that do not sit above plentiful groundwater. Howitt said food banks in some areas are already seeing greater demand.
The drought, now in its fourth year, has already affected many of the state's crops, including almonds, citrus trees, wine and others.