It is located in south central Minnesota within Blue Earth, Cottonwood, Faribault, Freeborn, Jackson, Martin, Watonwan counties and northern Iowa. There are 21 municipalities in the watershed of which the city of Mankato is the largest. The Blue Earth River major watershed area is approximately 1,550 square miles or 992,034 acres. The watershed is subdivided into 115 minor watersheds. The minor watersheds range in size from 2,197 acres to 30,584 acres with the mean size approximately 8,626 acres.
Agriculture is the predominant land use within the watershed.
The Blue Earth River and its tributaries, public and private drainage systems, lakes and wetlands, define the drainage network of the major watershed. The Blue Earth River flows north to its confluence with the Minnesota River at the city of Mankato in Blue Earth County. The total distance of the stream network in Minnesota is 1,178 miles of which 414 miles are intermittent streams and 764 miles are perennial streams.