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The Mustinka River begins its course southwest of Fergus Falls in southwestern Otter Tail County and flows toward the south into Grant County, where it continues through Stony Brook Lake and Lightning Lake.
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 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 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 Buffalo River Watershed covers more than 1,100 square miles in portions of Becker, Clay, Otter Tail, and Wilkin counties, with a small portion of its headwaters in the White Earth Reservation.
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 North Fork Crow River Watershed covers 949,107 acres.
The Mississippi River - St. Cloud Watershed covers 691,200 acres (1,080 square miles) in the south-central part of the Upper Mississippi River Basin. The watershed includes all or parts of the counties of Benton, Meeker, Mille Lacs, Morrison, Sherburne, Stearns, and Wright.
The Mississippi River - Winona Watershed covers 419,200 acres in the southeast Minnesota counties of Wabasha, Winona, and Olmsted. A majority of the watershed is cropland, with forest and grassland covering large portions as well.