Wheat futures also fell on a larger-than-expected crop forecast for US spring wheat despite drought in the northern Plains crop belt.
Chicago Board of Trade November soybean futures settled down 33 cents at $9.40-1/4 per bushel after hitting $9.38-1/2, the contract's lowest since June 30.
CBOT December corn ended down 15-1/4 cents at $3.71 per bushel after touching $3.70-1/4, its lowest since Sept. 30.
The USDA projected the US corn yield at 169.5 bushels per acre (bpa), below its previous forecast of 170.7 but above an average of trade estimates for 166.2 bpa.
For soybeans, the USDA put the yield at 49.4 bpa, above its previous forecast of 48.0, surprising analysts who expected a reduction.
Both figures implied larger harvests than most analysts expected, given planting delays and dry conditions in parts of the Midwest.
"They (USDA's yield estimates) are, I would say, shockingly bearish. They caught the trade leaning the wrong way. They caught the funds leaning the wrong way," said Don Roose, president of US Commodities.
"The biggest issue is the rise in soybean yield, and no doubt there will be adjustments down the road," said Rich Nelson, chief strategist at Allendale Inc.
Others noted that US crop weather has improved in August, the most important month for determining soybean yields.
"Though not quite to the record of 2016/17, this still could be a huge (soybean) crop, especially with such large acreage," Alex Norton of Beeson & Associates wrote in a client note.
CBOT wheat futures fell about 4 percent, with the September contract down 19 cents at $4.40-1/2 per bushel, after the USDA's estimate of the US spring wheat crop topped trade expectations.
MGEX December spring wheat fell 30 cents to $7.15-1/2 after hitting $7.15, its lowest since June 29.
The USDA estimated US production of spring wheat other than durum at 402 million bushels, down from 423 million in July but well above the average trade estimate of 393 million.
"Given the disaster spring wheat crop and horrible conditions, this modest decline was a surprise to traders," Norton said.