Its source is in southern Polk County east of the village of Clear Lake.
[2] Subsequently, the Willow River Power Company built a hydroelectric facility to utilize the same head of water, but the head was substantially decreased when the United States built the Red Wing Dam 30 miles (48 km) downstream on the Mississippi River.
In its upper reaches it flows through the Cylon Marsh State Wildlife Area.
Each spring rainbow and brook trout are stocked at various locations along the river.
[3] The status of the Willow River as a non-navigable stream figured in constitutional litigation over whether a head of water to which it contributed was a property interest for purposes of the Fifth Amendment, in United States v. Willow River Power Co..[4]