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.

Cow Creek is considered to be both a second and third order tributary of the Palouse River in the southern part of Latah County and northern part of Nez Perce County, Idaho. The creek flows primarily southwest for about 18.5 miles before it enters Union Flat Creek.  A sewage lagoon facility is located along Cow Creek just downstream of the City of Genesee.

Low flow periods in Cow Creek between July and September coincide with periods of diurnal dissolved oxygen exceedances in both the intermittent and perennial reaches of the watershed. This TMDL is intended to manage in-stream phosphorus concentrations, reduce aquatic plant growth, and enhance dissolved oxygen during the mid- to late-summer critical flow period between July and September.

The Genesee wastewater treatment lagoon is the only point source permitted to discharge in the Cow Creek watershed. In February 2005, the U.S. Environmental Protection Agency (EPA) issued a National Pollutant Discharge Elimination System (NPDES) permit to the City of Genesee allowing discharge year round. Historically, the city only discharged from November to July. The city anticipated the need to discharge year-round due to increasing influent flows and required lining of the lagoons to eliminate seepage. The new permit requires the city to monitor effluent quality and the receiving surface waters of Cow Creek. Surface water monitoring is required for temperature, pH, total phosphorus, and ammonia.

This TMDL provides a wasteload allocation for the wastewater treatment lagoon for total phosphorus of 0.60 kilograms/day during the annual critical low flow period of June through September.

The primary nonpoint sources of pollutants in the Cow Creek watershed are non-irrigated croplands and grazing lands. The entire length of Cow Creek and its tributaries typically receive pollutants from agricultural fields during rainfall and snow melt. Nutrients associated with sediment also enter the creek at these times from fields and unstable banks. During the summer low-flow periods, portions of Cow Creek experience temperature increases and low dissolved oxygen concentrations.

A TMDL was developed for nutrients (total phosphorus) for Cow Creek.  TMDLs were not developed for temperature or habitat alteration.  It is recommended that Cow Creek remain on the §303(d) list for temperature and that a temperature TMDL be deferred until additional data can be collected to determine if a TMDL is needed.

The EPA does not consider habitat alteration to be a pollutant as defined by the Clean Water Act.  Since TMDLs are not required for water bodies impaired by pollution but not pollutants, a TMDL was not developed for habitat alteration.