Heads on the north slope of Hickory Ridge, flow south to join the Little River northeast of Bell City.
Historically, the name Whitewater River applied to a 120 km (75 mi) long stream that headed near the community of Womack in St. Francois County, flowing south through Perry County, Bollinger County, and Cape Girardeau County before entering the Little River near Bell City. However, in the early 20th century, the Little River Drainage District constructed the Headwater Diversion Channel, which bisected the Whitewater River, causing the northern section of the stream to be diverted into the diversion channel, and separating the southern portion from its original headwaters. In 2007, the Board on Geographic Names (BGN) approved a proposal to rename the two portions Upper Whitewater Creek and Lower Whitewater Creek