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.

Three stream segments in the Idaho Falls Subbasin are listed on the §303(d) list. The hydrology of the Idaho Falls Subbasin is dominated by the Snake River and its associated diversion structures for irrigation of farmland on the Snake River Plain.

Flow in the South Fork Snake River is controlled upstream of the subbasin by Palisades Reservoir. Numerous irrigation diversions also influence flow on the South Fork Snake River. A small section of the South Fork Snake River at the eastern-most border of the subbasin is §303(d) listed for flow alteration, but a TMDL was not prepared for this. Flow is not considered a “pollutant” under the Clean Water Act, and TMDLs are not required for pollution that isn't caused by a “pollutant.” However, it is recommended that this stream reach remain on the §303(d) list for flow alteration.

South Fork Willow Creek has been §303(d) listed for sediment; however, this stream no longer exists as a natural watercourse. Since the construction of Ririe Dam in the 1970s, the flow in the Willow Creek/Sand Creek complex has been controlled for irrigation. Willow Creek, including both the North Fork and the South Forks, has been converted to canal conveyance structures with straightened channels and riprap style bank reinforcement. No water flows in these channels during the non-irrigation season. Therefore, it is recommended that South Fork Willow Creek be removed from the §303(d) list.