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 Big Lost River Subbasin Assessment and TMDL describes nine water bodies that are listed on the 1996 and 1998 §303(d) lists prepared by the state of Idaho. These water bodies are considered water quality limited and may not meet their beneficial uses as defined by the state of Idaho water quality standards. The subbasin assessment portion of this document examines the current status of these §303(d) listed waters and defines the extent of impairment and causes of water quality limitation throughout the subbasin. The loading analysis quantifies pollutant sources and allocates responsibility for load reductions needed to return listed waters to a condition of meeting water quality standards.

The Big Lost River Subbasin, isolated from surface connection with the Snake River, is one of four watersheds in central Idaho known as the Sinks Drainages. Surface flow not utilized for irrigation infiltrates to ground water, which is conducted southwest toward the Thousand Springs reach of the Snake River near Hagerman, Idaho, where spring flow emerges. Native fish populations, water quality, and riparian habitat conditions are issues of concern in the subbasin. The cumulative effects of irrigation diversion, alteration of vegetation by grazing in riparian areas, human-caused stream alterations, historic mining practices, roads, residential and municipal development, and past timber harvest have combined to impact water quality and aquatic life in the watershed.

Twelve TMDLs were developed to address issues of temperature exceedance of water quality standards on eleven streams (two segments on Antelope Creek). Sediment TMDLs were prepared for the streams with temperature exceedances with the exception of Warm Springs Creek and the main Big Lost River from its origin at the confluence of the North and East Forks of the Big Lost River to Chilly Buttes. Sediment TMDLs were prepared for two additional streams that did not have sufficient temperature data to determine TMDLs for thermal loading: Twin Bridges Creek and Thousand Springs Creek.

TMDLs were not prepared for habitat and flow alteration. These are considered "pollution," but not "pollutants," and TMDLs are not required for water bodies impaired by pollution, but not by specific pollutants. A TMDL is only required when a pollutant can be identified and in some way quantified.