Section 303(d) of the Clean Water Act establishes requirements for states and tribes to identify and prioritize water bodies that are water quality limited (i.e., water bodies that do not meet water quality standards). States and tribes must periodically publish a priority list of impaired waters, currently every two years. For waters identified on this list, states and tribes must develop water quality improvement plans known as total maximum daily loads (TMDLs) that establish allowable pollutant loads set at levels to achieve water quality standards.

The Lemhi River TMDL is intended to address water quality concerns on seven streams and the Lemhi River. These surface waters within the subbasin have been identified as having a beneficial support status less than full support. Two additional streams that are listed as water quality impaired did not have TMDLs written because they are dewatered for irrigation.

The Lemhi River has been identified as providing critical spawning and rearing habitat for two federally protected anadromous species: steelhead trout and spring/summer chinook salmon. The Lemhi River and its tributaries also provide important historic and/or current habitat for federally protected resident and migratory bull trout as well as westslope cutthroat trout, which have been petitioned for listing under the Endangered Species Act.

TMDLs have been developed to address sediment in Bohannon Creek, Eighteenmile Creek, Geertson Creek, Kirtley Creek, Sandy Creek, McDevitt Creek, and Wimpey Creek, and to address fecal coliform bacteria in the Lemhi River. Though Bohannon, Eighteenmile, Geertson, Hawley, Mill, Sandy and Wimpey Creeks are listed for nutrients as well, no conditions within the streams have been observed that necessitate the writing of TMDLs for nutrients based on narrative state water quality standards.

The primary anthropogenic source of sediment having a deleterious effect on beneficial use support status within the seven streams listed for sediment was identified as sediment from stream bank erosion.