The Whitewater River is a Minnesota tributary of the Upper Mississippi River reaching its mouth in Winona County, opposite Buffalo, Wisconsin. It is located in the Driftless Area of Minnesota. The nearest towns are Altura, Saint Charles and Elba. The region hosts endangered native dry oak savannas, semiforested areas that seem to have been dependent on fire for their well-being.
The state maintains Whitewater State Park on the upper reach of the main branch, on the Middle Branch and on Trout Run Creek. Crystal Springs Fish Hatchery is located on the lower portion of the South branch.