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.

Lindsay Creek is a third order tributary to the Clearwater River. The main stem of Lindsay Creek originates from springs at a wetland just below Mann's Reservoir and flows northwest to its confluence with the Clearwater River in Lewiston, Idaho.

DEQ is establishing TMDLs to control bacteria, excess nutrients, and sediment in Lindsay Creek. Monitoring conducted in April 2005 indicates that the development of a bacteria TMDL is needed to comply with Idaho water quality standards. A nutrient TMDL has been developed to initiate protective ground water quality management actions, reduce nitrogen loading to the creek, and address the effects on the cold water aquatic life in the creek.

A sediment TMDL has been developed to maintain protection of existing fish populations and restore habitat conditions in the watershed. The sediment TMDL allocates approximately 79% of the load capacity to nonpoint sources and provides a 3% wasteload allocation for potential inclusion into the city of Lewiston's future municipal National Pollution Discharge Elimination System (NPDES) permit.

There are no known point sources that discharge to Lindsay Creek at this time. Nonpoint sources of bacteria in the Lindsay Creek watershed include livestock, septic systems, pets, and wildlife. In agricultural areas, the application of fertilizers to crops is a source of nutrients to subsurface waters as well as to Lindsay Creek through direct runoff. Manure from pets, wildlife, and livestock can contribute nutrients to the creek as well.

As a result of further water quality sampling and/or inconclusive data, it is recommended that temperature and dissolved oxygen be removed from the list of pollutants impairing Lindsay Creek and that no TMDLs be developed for these pollutants.

Since flow alteration and habitat alteration are not pollutants that can be quantified and allocated for loadings, TMDLs have not been developed for them.