The gentle to moderate flowing river drops an average of 3.4 ft/mile from Chatfield, Minnesota, to its pour point in the Mississippi River into Navigation Pool 7 just south of La Crosse, Wisconsin and east of Hokah, Minnesota.

A mile and a half north of Lanesboro, Minnesota it is joined by the South Branch Root River.

[6][7] The South Branch Root River rises in Mower County as agricultural drainage ditches, which disappear underground, re-emerging as a much cooler stream[8] at Mystery Cave near Preston, Minnesota.

It begins in Fountain and continues through Lanesboro, Whalan, Peterson, Rushford, and Houston.

As a result of the 2007 Midwest flooding, the river rose to 19 feet (5.8 m), about a foot short of the height of the dike protecting the town of Houston.