Corn futures are up 15% for the month as forecasts for heavy rain across major farming areas pose risks to more delays in planting.
The crop is leading a surge in most soft commodities this month.
Corn futures settled down less than 1% on Wednesday, after hitting their highest level since June 2016 earlier in the day, while other key commodities like soybeans and wheat also trend upward. Soybean futures settled up 1.5% and wheat futures settled down 3%, after being up almost 3% earlier in the day.
"Now the market's in a situation where you're going to have very low inventory levels, very slim plantings, and by next spring it could be a real issue," Peter Boockvar, chief investment officer of Bleakley Advisory Group, told CNBC's "Squawk Box" on Wednesday.
Corn futures are up more than 15% this month, while soybean futures have risen more than 2% in May and wheat futures are up more than 12% this month.
In a record-breaking wet spring, flooding in key farming regions has caused unprecedented delays to planting, causing lower-than-expected inventory levels. In corn, 58% of the intended planting has been done, compared with 90% at this point historically. For soybeans, only about 30% has been planted, versus about 65% normally, said Boockvar.
"It's never been this delayed," he said, citing USDA data going back to 1980.
In a note to clients earlier this month, CitiGroup said: "We see ongoing bullish price risks for corn if wet weather persists through May/early June, as farmers may reduce corn area and shift sowing towards late-planted beans, a bearish risk for the oilseed complex especially if the White House subsidizes soy production. We are more neutral wheat, which has been dragged higher by corn."
Alongside bad weather, the U.S.-China trade war is further complicating the planting picture. Before trade tensions heightened, China was responsible for more than 60% of soybean exports.
Last week, President Donald Trump announced a $16 billion aid package to help farmers, a group that played a major role in Trump's 2016 victory and have been hit by the trade war. The farm aid legislation will compensate farmers, mainly in cash payments, for about 10 months of trade war loses.
The rise in commodity prices will also have an impact on restaurants, which have thin margins as it is, said Boockvar. Food prices are about 30% of a restaurant's cost base with labor making up pretty much of the rest of the balance, he said.
"There's not much room to handle a rise in food prices," said Boockvar.
— with reporting from CNBC's Michael Bloom.