The Rabbit River is located in the Bois de Sioux watershed (589 square miles with 321.4 square miles located within Minnesota) within the Red River of the North basin. In 1996, the MPCA identified a 22.24 mile reach of the Rabbit River as being impaired for aquatic life due to excessive turbidity. The reach in question (AUID 09020101-502) runs from the Grant County/Wilkin County line to the Bois de Sioux River. The watershed has been extensively drained. Land use within the watershed is dominated by agricultural crop production. In 2001, an estimated 85.43% of the watershed was used for crop production.
The TMDL study was initiated in 2007 with a cooperative relationship between the Bois de Sioux Watershed District and the Detroit Lakes Regional Office of the MPCA. The TMDL is based on Load Duration Curves and Soil and Water Assessment Tool (SWAT) modeling. The TMDL report has been completed and EPA has approved it.