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The Sauk River Watershed covers 667,200 acres (1,043 square miles) and extends from the Mississippi River near St. Cloud to within 3 miles of Alexandria.

The Des Moines River - Headwaters Watershed is located in southwestern Minnesota and covers approximately 1,334 square miles, including parts of Lyon, Pipestone, Murray, Cottonwood, Nobles, Jackson, and Martin counties.

The Lower Des Moines River Watershed is located in southwestern Minnesota. It covers approximately 703,000 acres.

The Shell Rock River begins at Albert Lea Lake in Freeborn County in south-central Minnesota, a few miles from the Iowa border. It flows 113 miles into Iowa, where it enters the Cedar River. In Minnesota, the Shell Rock drains 246 square miles (160,000 acres), all in Freeborn County.

The Crow Wing River Watershed is located in north-central Minnesota and covers approximately 1,946 square miles within the counties of Becker, Cass, Clearwater, Crow Wing, Hubbard, Morrison, Otter Tail, Todd, and Wadena.

The North Fork Crow River Watershed covers 949,107 acres.

The Pomme de Terre River begins cool and clear in Otter Tail County, bordered by wooded hills and grassy meadows. It flows south through several lakes; as the river nears its mouth, it is bordered by eroding banks, becoming increasingly muddy before discharging into the Minnesota River at Marsh Lake.

The Cedar River Watershed in Minnesota encompasses 454,029 acres in Mower, Freeborn, Dodge, and Steele counties. This watershed covers prime agricultural land with many streams and drainage ditches flowing into the river.