The bus stalled at 158th between East End and Greenwood streets.
Witnesses say crews from Country Club Hills were assisting the Dolton Fire Department in removing the children from the bus.
The children, who were being transported home from Dirksen Middle School in Calumet City, were ferried to dry land two at a time in a small boat.
There are no reports of any injuries.
"This intersection has been known to flood every time we have major rain," said Dolton Fire Department Lieutenant Dave DuVall. "We've been here about 4-5 times today for different cars going around barriers thinking they can make it through the water."