Farmers in Manitoba and Saskatchewan fear harvests may be lost this year now that overland flooding has made some fields look more like lakes.

Doug Chorney

Doug Chorney, president of Keystone Agricultural Producers, examines his flooded field near Selkirk, Man., on Wednesday. (Karen Pauls/CBC)

Doug Chorney of Manitoba-based Keystone Agricultural Producers estimates at least 800,000 hectares of farmland will likely go unseeded across both provinces this year.

Crops that have already been planted are drowning at this point, he said, adding that anything that survives likely won't yield its full potential.

"It's heartbreaking when you put so much work into growing a crop, you grow the best seed you can buy, and you fertilize it properly, and then you have weather like this," Chorney said from his flooded wheat field near Selkirk, Man., on Wednesday.

"It's just terrible."

A colder than usual winter across the Prairies resulted in a late spring planting season, and many farmers had to deal with record high rainfall in June.

This past weekend, an intense storm system dumped between 100 and 200 millimetres of rain on southeast Saskatchewan and southwest Manitoba, causing overland flooding in some places.

"Because it was so wet, and now I'm told there's white caps on windy days on their fields, so it looks like a lake," Chorney said.

Saskatchewan Premier Brad Wall estimates the flooding could cost in excess of $360 million, similar to what it cost in the 2011 flood. However, that figure does not include farm losses, which are certain to be significant and widespread.

"Pretty tough to grow a crop or harvest a crop if it's under water. That will be a challenge," Wall said.

Farmers in the Prairies enjoyed bumper crops last fall, but a slowdown in rail traffic over the winter means grain may still be in some producers' bins, waiting to be sold and shipped.

Manitoba Agriculture Minister Ron Kostyshyn said farmers in his province have crop insurance, but he knows that won't make up for lost income.

"I think we'll be very happy to see sunshine for the next three months," he said. "Unfortunately, nobody is in charge of Mother Nature."