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.

Since Winchester Lake and Lapwai Creek lie within the Nez Perce Reservation, a Memorandum of Agreement was developed among the Nez Perce Tribe, the U.S. Environmental Protection Agency (EPA), and DEQ to develop TMDLs for these water bodies.

Winchester Lake and its watershed lie entirely within the Nez Perce Reservation. The lake sits approximately 30 miles southeast of Lewiston, Idaho, and 0.5 mile south of the town of Winchester. Winchester Lake is a manmade reservoir and is the focal point of Winchester Lake State Park. Upper Lapwai Creek is the largest tributary to the lake.

Blue-green algal blooms develop frequently in the lake, and periodic fish kills have occurred. Winchester Lake is severely eutrophic. Excessive sediment, degraded habitat, and elevated temperatures are also having an adverse effect on Upper Lapwai Creek.

In the past, bacteria concentrations in Winchester Lake were quite high, likely due to improper sewage disposal. These problems have been corrected and data indicate bacteria are not a problem in Winchester Lake. However, data do indicate that fecal coliform levels exceed state water quality standards in the Lapwai Creek drainage. Since Lapwai Creek is the largest contributor to the lake, and since it appears that Winchester Lake meets bacteria standards, it was concluded that a bacteria TMDL for Upper Lapwai Creek would be adequately protective of both the creek and lake.

Past water quality studies of Winchester Lake have indicated that excessive levels of nutrient compounds in the lake and lake sediment cause nuisance algae growth that depletes oxygen in the lake's deeper waters. A nutrient TMDL has been developed that should reduce phosphorus loading and also increase dissolved oxygen levels. A nutrient TMDL for Upper Lapwai Creek was also developed.

Sediment is degrading the water quality of Upper Lapwai Creek and Winchester Lake; sediment TMDLs were developed for both. A temperature TMDL for Upper Lapwai Creek was established to address impaired salmonid spawning and rearing uses.

Fish caught in the lake were tested for pesticides. While some pesticides were detected in tissues samples, data analysis indicated that the risk of health effects from eating these fish is very low, and does not exceed risk levels used to establish state water quality standards. As a result, a TMDL for pesticides was not written.

Both water bodies are listed for flow and habitat alteration. However, the EPA does not believe that flow and habitat alteration are pollutants 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 or habitat alteration.