The federal Clean Water Act requires that states and tribes restore and maintain the chemical, physical, and biological integrity of the nation's waters. States and tribes must adopt water quality standards necessary to protect fish, shellfish, and wildlife while providing for recreation in and on the waters whenever possible.

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 South Fork Coeur d'Alene River watershed is in the center of the Coeur d'Alene Mining District. Most streams in the subbasin are §303(d) listed for metals and sediment, and one stream is listed for habitat alteration. The trace (heavy) metals impacts to water quality were addressed in the Coeur d'Alene Basin Metals TMDL. (In 2003 the Idaho Supreme Court determined that the Coeur d'Alene Basin Metals TMDL was void because it was not promulgated according to the rulemaking requirements of the state Administrative Procedures Act).

Sediment is listed as a pollutant for 14 stream segments in the watershed. Sediment has its source in mine waste piles, urban land use, road erosion, encroachment on stream channels and floodplains, and encroachment of towns and mining facilities. Impairment of the cold water use has been demonstrated in the low diversity of macroinvertebrates and in low trout abundance. These impacts are the result of both metals and sediment. Impacts of the two pollutants are not easily differentiated. However, the impaired segments of the South Fork Coeur d'Alene River Subbasin typically have low residual pool volumes as compared to segments with high trout abundance. These data indicate sediment is filling pools. Therefore, a sediment TMDL was developed for all of the sediment listed segments of the South Fork Coeur d'Alene River Subbasin.

Canyon Creek is listed for habitat alteration as well as sediment. The U.S. Environmental Protection Agency considers certain unnatural conditions, such as habitat alteration, that are not the result of the discharge of specific pollutants as "pollution." Since TMDLs are not required for water bodies impaired by pollution, but not specific pollutants, a TMDL for habitat alteration was not developed.