It is located in south central Minnesota within Blue Earth, Brown, Cottonwood, Le Sueur, Nicollet, Redwood, Renville, Sibley and Watonwan counties. There are 20 municipalities in the watershed of which the city of Mankato is the largest. The Middle Minnesota River major watershed area is approximately 1,347 square miles or 862,060 acres. The watershed is subdivided into 104 minor watersheds. The minor watersheds range in size from 1,297 acres to 28,760 acres with the mean size approximately 8,289 acres.
Agriculture is the predominant land use within the watershed.