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 American Falls Subbasin covers 2,869 square miles in southeast Idaho; much of which is within the Fort Hall Indian Reservation. American Falls Reservoir is the predominant water body in the subbasin and provides both irrigation water and electricity.

TMDLs were developed for nutrients on 17 water bodies in the subbasin and for sediment on nine water bodies. TMDLs were also developed nutrients and sediment for six point sources of pollution. Two of the point source wasteload allocations (sediment from the city of Blackfoot's storm water runoff and nutrients from the Aberdeen wastewater treatment plant) require a reduction from current estimated wasteloads.

American Falls Reservoir and McTucker Creek are §303(d) listed for flow alteration. However , the U.S. Environmental Protection Agency does not believe that flow alteration is a pollutant as defined by the Clean Water Act. Since TMDLs are not required for water bodies impaired by pollution but not pollutants, TMDLs were not developed for flow alteration.

TMDLs were also not established for dissolved oxygen or bacteria. Dissolved oxygen was listed for the Snake River and American Falls Reservoir. Data did not indicate dissolved oxygen was a problem in Snake River, and it was assumed that a nutrient TMDL will bring dissolved oxygen levels in the reservoir into compliance with water quality standards. There were insufficient data to determine if bacteria impair recreation in Bannock Creek, so more data will be collected to determine beneficial use support.

The document recommends that American Falls Reservoir be delisted for sediment and the Snake River be delisted for dissolved oxygen and nutrients. American Falls Reservoir and the Snake River should be listed for temperature on future §303(d) lists. The document also recommends that Danielson Creek, Hazard Creek (Little Hole Draw), and Sunbeam Creek be added to future §303(d) lists.