Wheat futures fell on technical selling and corn was modestly lower.
Chicago Board of Trade November soybeans settled up 3 cents at $9.58-1/4 per bushel. CBOT December wheat ended down 6 cents at $4.42 a bushel and December corn fell 1-1/4 cents at $3.48-1/4 a bushel.
Soybeans firmed a day after the November contract notched a near three-week low.
"You've got a combination of increasing freight rates and (widening) basis levels scaring the farmer from making sales. Plus you've got some harvest delays," said Brian Hoops, president of Midwest Market Solutions.
Rains crossed parts of Iowa, Minnesota and Wisconsin in the last day, with light showers crossing areas of Missouri, Illinois and Indiana.
Fears that dry weather might limit Brazilian soy plantings lent support. Industry group Abiove estimated Brazil's 2017-18 soybean crop at 108.5 million tonnes, down from its forecast last month of 113.8 million tonnes.
Corn futures declined but pared losses after the December contract dipped to a three-week low of $3.46. Traders noted chart support at the contract low of $3.44-1/4, set on Aug. 31.
Corn was anchored by better-than-expected yield reports from the early harvest and concern that the US Department of Agriculture might raise its US corn yield forecast in its next monthly supply/demand report on Oct. 12.
"Despite earlier concerns, the season has shaped up pretty well and the harvest is advancing at a steady rate," said Phin Ziebell, agribusiness economist at National Australia Bank.
Commodity brokerage INTL FCStone this week raised its forecast of the US corn yield to 169.2 bushels per acre, from 166.9 a month earlier. The firm also raised its US soybean yield forecast, to 49.9 bpa from 49.8 previously.
Wheat prices remained capped by export competition created by a record Russian harvest this year, a factor underscored by the latest Egyptian purchase of Russian wheat on Tuesday.
Also bearish, beneficial rains this week have bolstered prospects for the 2018 US hard red winter wheat crop in the southern Plains and soft red winter wheat in the Midwest.