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.

Both fine sediment and coarse sediment impair salmonid spawning and rearing in Cottonwood Creek. TMDLs were developed for both. A TMDL was also developed for temperature to protect steelhead salmonid spawning and other cold water aquatic life. The temperature TMDL established percent reduction targets that are linked to percent increase in shade.

Nutrient and dissolved oxygen TMDLs were combined. An assumption was made that by meeting the instream nutrient target the dissolved oxygen standard will also be met.

A TMDL for bacteria was developed. The Cottonwood wastewater treatment plant was not a significant source of bacteria loading; therefore, its wasteload allocation was left at its existing permitted limit. Significant sources of bacteria in the watershed include animal wastes, septic tank failures, and cattle in streams.

An ammonia TMDL was developed that requires a five percent reduction in total ammonia during November through April. The ammonia TMDL only addresses the toxicity effects of ammonia; the nutrient effects of ammonia are evaluated in the nutrient TMDL.

Flow and habitat are identified on the §303(d) list; however, the TMDL does not address these issues as they are currently not required to be addressed under the Clean Water Act.