The analysts estimated that between 300,000 and 800,000 acres in traditionally fertile areas of Iowa and Nebraska for corn and soybeans could be hit by flooding.
"It is important," said Dan Basse, president of AgResource Co. "We cannot afford to lose any acres. It is another calamity for the market."
Rain in eastern areas of the Corn Belt were already threatening to reduce the size of the crop this fall. Farmers who have been unable to plant corn due to rain were considering switching to different crops or collecting insurance payments, then trying again next year.
Massive floods in the South submerged some farmland last month after the Mississippi River burst its banks.
The Agriculture Department said farmers had planted 86 percent of their anticipated corn acreage as of May 29. That was 9 percentage points behind the 5-year average.
Farmers still have nearly 13 million acres of corn left to sow, including about 3 million in Ohio, if they want to meet their original planting intentions.
Growers in areas west of the Mississippi had enjoyed good weather during the planting season, but the flooding threatens to undo some of the progress they have made.
In Iowa, corn planting was 98 percent completed. Farmers in Nebraska have planted 94 percent of their corn crop.
Total planted corn acreage in Iowa and Nebraska, the largest and third-largest corn producing states respectively, was expected to be 23.4 million acres this year.
The high water levels already were affecting some areas of agriculture, even though fields remained dry.
Agribusiness company Cargill was laying sandbags and building a berm or sloping wall around a corn mill in Blair, Nebraska and had stopped accepting loads of corn and soybeans at an elevator in Council Bluffs, Iowa due to the rising rivers.