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Brutal drought to bring even higher food prices

File photo of a rancher inspecting a dead cow in Colorado.
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Disease and harsh weather continue to push up food costs for consumers. But they're likely to go even higher from the ongoing drought hitting much of the Southwest.

The U.S. Department of Agriculture's Economic Research Service said that California's drought could increase food price inflation above the historical average in the weeks ahead.

"It doesn't take long for the effects of what's happening at the farm level to transfer to the checkout counter," said Annmarie Kuhns, a researcher at the USDA, told CNBC. "It's usually just about a month for the impact to take hold."

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The Golden state produces half of the nation's fruits and vegetables, and most of its high-value crops such as broccoli, tomatoes and artichokes.

But the drought has been pushing the cost of water higher, forcing farmers there to leave fallow hundreds of thousands of acres of land, and making foods more expensive.

Timothy Richards, a professor of agribusiness at Arizona State University, told CNBC in April that he believes between 10 and 20 percent of the supply of certain crops from the state could be lost due to the drought.

Because of that, Richards said there would be price increases on such items as berries, broccoli, grapes, melons, tomatoes, peppers and packaged salads.

"I would expect a 28 percent increase for avocados and 34 percent for lettuce," he said.

Prices climbing

Meanwhile, prices for fresh fruit rose for a third consecutive month in May, according to the U.S. Department of Agriculture. The USDA blamed a citrus greening disease that's afflicting Florida's orange and grapefruit trees.

Also to blame—and in a touch of irony—drought-ridden California suffered a recent cold snap in the southern part of the state that wiped out many orange and lemon crops.

Overall, fruit prices rose 2 percent in May from April and 7.3 percent from a year ago at this time, according to the USDA.

The USDA has revised upward its estimate on inflation for fruit prices and now expects it to jump 6 percent in 2014, up from its May projection of 4 percent.

Overall, food prices rose half a percent in May, which is the largest hike since August 2011, according to the U.S. Labor Department.

USDA's Kuhn said imports of food products could help ease the strain on consumers but that there was no way to tell by how much.

Wheat crop hit hard

Shifting breakfast trends
Shifting breakfast trends

Besides California, states including Texas, Colorado, New Mexico, Arizona, Nevada and Oklahoma are in drought conditions. That's driven up beef prices 9 percent so far this year, and that could go even higher.

Wheat is getting hit particularly hard by the drought, according to the United States Drought Monitor.

Read MoreWhy your water bill will likely increase

Fifty-one percent of the winter wheat production in the United States was within an area experiencing drought on June 3, with wheat farmers in Oklahoma, Texas and Kansas hit the hardest.

As for the drought itself, parts of the Midwest and Central Plains got a break from crippling conditions this past week, but California continues to be in one of its worst dry spells on record.

Read MoreWhy so many Americans don't care about the drought

The nation as a whole saw a small decrease in the areas suffering from the worst kind of droughtwhich the Drought Monitor calls "exceptional."

In a bit of good news, 3.14 percent of the nation was experiencing exceptional drought last week, but it's down this week to 2.91 percent.

By CNBC's Mark Koba