"Some farmers may still grow crops on some of their land. Some farmers may face bankruptcy because of this," said Mike Wade, executive director of another industry group, the California Farm Water Coalition.
Democrats and Republicans in the state are sharply divided on how to deal with the crisis, and there is also division within the ranks of each party.
At the Republican-led U.S. House of Representatives, an emergency bill by several California representatives that would roll back environmental protections for fish in the fragile Sacramento-San Joaquin River Delta in order to allow more water to be pumped out in dry years passed on Wednesday roughly along party lines, 229-191.
The bill, which will be immediately sent to the Senate, has been harshly criticized by Brown, who called it "unwelcome and intrusive."
But supporters say environmental regulations caused the water shortages in the first place by limiting the amounts that can be pumped out of the delta when fish are threatened in drier years.
"It is unacceptable that vital water supplies are being forced out to the ocean instead of going to our cities," said Republican Rep. Kevin McCarthy, who represents agricultural and desert areas north of Los Angeles. "The issue demands immediate attention and today's vote represents House Republicans' commitment to putting California families over fish."
(Read more: Senate passes farm bill, sends to Obama to sign)
Ironically, the crisis is unfolding after an all-time banner year for California agriculture, with statewide production valued at $43.5 billion in 2012. Most of that comes from California's Central Valley, a flat, fertile region stretching 450 miles north-south from Redding to Bakersfield.
Farm districts representing about half of irrigated agriculture in that region have reported that they already expect to fallow 385,000 acres this year because of the water shortage, Wade said.
Extrapolating to the remainder of the Central Valley, Wade said his organization expects the full amount of irrigated land removed from production this year will easily top 500,000 acres of the region's total of approximately 6 million acres.
The Farm Bureau is similarly projecting between 400,000 and 500,000 acres of irrigated land being fallowed, Wenger said.
Broccoli and cantaloupes hit hard
Hardest hit would be such annual row crops as tomatoes, broccoli, lettuce, cantaloupes, garlic, peppers and corn. Wade said consumers can also expect higher prices and reduced selection at grocery stores, particularly for products such as almonds, raisins, walnuts and olives.
He said the potential total value of unplanted crops was hard to calculate. But his group estimates the overall impact of idled farmland will run roughly $5 billion in direct costs of lost production and indirect effects through the region's economy.
An economic toll of that magnitude would put about 40 percent of all agricultural jobs in the Central Valley at risk, or about 117,000 people directly employed in farm production, processing and transportation, he said.
Wenger declined to venture an estimate of economic losses. But he said, "It's going to be a sizable number that we've never seen before, and it's going to ripple through the local economies, especially where agriculture is the name of the game."
By contrast, a California drought in 2009 resulted in an estimated 269,000 acres of cropland idled, $368 million in lost farm revenues and total reduced economic output of $796 million, according to a study from the University of California at Davis cited by Wade. Nearly 10,000 jobs were lost.
Steve Lyle, a spokesman for the state Department of Food and Agriculture, said the agency is working with UC Davis to develop real-time impact assessments.
"We are anticipating significantly higher economic impacts, compared to the 2009 drought, for the agricultural sector," he said.
The current water shortage could be made worse by the fact that many farmers have switched from annual field crops to orchard-style produce, such as almonds and olives, which cannot simply be left fallow from one year to the next.
Many growers face the choice of either shutting off irrigation to their older, less-producing trees to save the younger ones, or spreading less water across their groves and accepting smaller overall yields.
Orange and lemon growers, who just weathered a damaging week-long blast of freezing temperatures in December, are fairly safe for now but worried about running short of water for next year's crop, said Joel Nelsen, president of California Citrus Mutual.
The cold snap cost the Central Valley growers, who account for most of the nation's fresh citrus fruit, about $441 million in lost revenues, out of about $1.5 billion in annual production, the trade group said.
Still, the losses paled in comparison with a severe freeze in December 1990 that damaged citrus trees so badly that growers lost two years of production.
(Read more: 'Serious' threat to Florida citrus crop)
Livestock producers are facing their own drought-related difficulties, including scant winter rain they rely on to grow grass for grazing their herds, industry officials say. Beef producers are being forced to ship much of their stock East, while dairy producers face higher costs to purchase hay and feed.