It is located in south central Minnesota within Blue Earth, Brown, Cottonwood, Jackson, Martin, and Watonwan counties. There are 12 municipalities in the watershed of which the city of St. James is the largest. The Watonwan River major watershed area is approximately 878 square miles or 561,620 acres. The watershed is subdivided into 59 minor watersheds. The minor watersheds range in size from 2,014 acres to 41,138 acres with the mean size approximately 9,519 acres.
Agriculture is the predominant land use within the watershed.
The Watonwan River and its tributaries, public and private drainage systems, lakes and wetlands, define the drainage network of the major watershed. The Watonwan River flows from the west to its confluence with the Blue Earth River about one mile south of the Rapidan Reservoir in Blue Earth County. The total distance of the stream network is 1,074 miles of which 685 miles are intermittent streams and 389 miles are perennial streams.