Official Government Website

Clearwater River (South Fork) Subbasin

Data Details
Hydrologic Unit Codes 17050112 17060305
Size 1,175 square miles (752,000 acres)
Water Bodies with EPA-Approved TMDLs (Category 4a) American River, Baldy Creek, Bear Creek, Beaver Creek, Big and Little Elk Creeks, Bridge Creek, Buffalo Gulch, Butcher Creek, Cottonwood Creek, Cougar Creek, Crooked River, East Fork American River, Elk Creek, Fall Creek, Gospel Creek, Granite Creek, Haysfork Creek, Huddleson Creek and tributaries, Johns Creek, Kirks Fork, Leggett Creek, Little Moose Creek, Long Haul Creek, Maurice Creek, Meadow Creek, Mill Creek, Moose Butte Creek, Mule Creek, Newsome and West Fork Newsome Creeks, Nugget Creek, Otterson Creek, Peasley Creek, Pilot Creek, Rabbit Creek, Red Horse Creek, Red River, Red Rock Creek, Relief Creek, Sally Ann Creek, Sawmill Creek, Schwartz Creek, Shebang Creek, Siegel Creek, Silver Creek, Sing Lee Creek, Sixmile Creek, Soda Creek, South and West Forks Red River, South Fork Clearwater River, South Fork Cottonwood Creek, Stockney Creek, Tenmile Creek, Threemile Creek, Trail Creek, Trapper Creek, Twentymile Creek and tributaries, West and East Forks Crooked River, Whiskey Creek, Williams Creek, Wing Creek
Beneficial Uses Affected Cold water aquatic life, salmonid spawning, primary and secondary contact recreation, agricultural water supply
Major Land Uses Timber harvesting, mining, grazing, outfitting and guiding, recreation, agriculture, cropland, pastureland, rangeland, forestland, urban/industrial
Date Cottonwood Creek TMDL Approved by EPA June 2000 EPA Approval Letter
Date Approved by EPA January 2021 Approval Letter

Subbasin Characteristics

The South Fork Clearwater River lies entirely within Idaho County, Idaho, and partially on the Nez Perce Reservation. The South Fork Clearwater River subbasin is located in north-central Idaho and encompasses an area of approximately 1,175 square miles (752,000 acres) with a 207-mile perimeter. The subbasin extends from the headwaters above Elk City (elevation 6,382 feet) to the confluence with the Middle Fork Clearwater River at Kooskia, Idaho (elevation 1,280 feet). The lower 12.8 miles of the South Fork Clearwater River main stem flow through the Nez Perce Reservation. The reservation encompasses 84,035 acres of the subbasin.

2000 Cottonwood Creek Watershed Assessment and TMDL

Cottonwood Creek is a 2nd-order tributary of the South Fork Clearwater River, located in Idaho County, Idaho. The Cottonwood Creek watershed is approximately 194 square miles (124,439 acres). Cottonwood Creek has been designated a high priority water quality limited segment. Portions of Cottonwood Creek lie within the Nez Perce Reservation. TMDLs for the remainder of the South Fork Clearwater River subbasin were completed in 2004.

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 solar load reduction targets that are linked to percent increases in shade.

Nutrient and dissolved oxygen TMDLs were combined under the assumption that meeting the instream nutrient target would result in also meeting the dissolved oxygen standard.

A TMDL for bacteria was also 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 5% 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.

2000 TMDL: Streams and Pollutants for Which TMDLs Were Developed

Stream Pollutants
Long Haul Creek Fine sediment, coarse sediment, temperature, total inorganic nitrogen, total phosphorus, bacteria
Lower Cottonwood Creek Fine sediment, coarse sediment, temperature, total inorganic nitrogen, total phosphorus, bacteria
Red Rock Creek Fine sediment, coarse sediment, temperature, total inorganic nitrogen, total phosphorus, bacteria
Shebang Creek Fine sediment, coarse sediment, temperature, total inorganic nitrogen, total phosphorus, bacteria
South Fork Cottonwood Creek Fine sediment, coarse sediment, temperature, total inorganic nitrogen, total phosphorus, bacteria
Stockney Creek Fine sediment, coarse sediment, temperature, total inorganic nitrogen, total phosphorus, bacteria
Upper Cottonwood Creek Fine sediment, coarse sediment, temperature, total inorganic nitrogen, total phosphorus, bacteria, ammonia

2003 Subbasin Assessment and TMDL

Eighteen stream segments and one lake in the South Fork Clearwater River subbasin were listed on the 1998 §303(d) list. TMDLs were completed in 2000 for six stream segments in the Cottonwood Creek watershed within the subbasin. This document addresses the remaining twelve listed streams and Lucas Lake.

Water temperatures are elevated above water quality standards at all monitoring locations throughout the subbasin. Logging, road building, mining, grazing, and agricultural activities have reduced shading of surface water. Point source contributions to water temperature increases are minor except for the effects of the effluent from the Grangeville wastewater treatment plant.

DEQ concluded that many unlisted stream segments throughout the subbasin need heat load reductions to meet water quality standards as well. Therefore, temperature TMDLs were established for an additional 58 unlisted stream segments throughout the subbasin.

Coarse sediment, which affects salmonid spawning, has degraded water quality in the upper basin. Nonpoint sediment sources in the South Fork Clearwater River are mainly agricultural and grazing areas (10–30 times natural background rates) and forested areas (2 times natural background rates). Point sources of sediment include five municipal wastewater treatment plants, suction dredge mining, and construction and industrial stormwater runoff.

Bacteria and nutrients in Threemile Creek greatly exceed state standards and US Environmental Protection Agency guidelines. The majority of the bacteria are thought to be from livestock grazing; the majority of the nutrients are from the Grangeville wastewater treatment plant.

As a result of this assessment, DEQ recommended that Lucas Lake and seven streams listed as impaired by sediment and one stream segment each listed as impaired by bacteria, nutrients, ammonia, and a lack of dissolved oxygen be removed from the §303(d) list.

2003 TMDL: Streams and Pollutants for Which TMDLs Were Developed

Stream Pollutants
South Fork Clearwater River Temperature, sediment
Threemile Creek emperature, bacteria, nutrients, dissolved oxygen, sediment
Butcher Creek Temperature, sediment
Dawson Creek Temperature
Little Elk Creek Temperature
Big Elk Creek Temperature
Buffalo Gulch Temperature
Newsome Creek Temperature
Beaver Creek Temperature
Nugget Creek Temperature
Sing Lee Creek Temperature
Cougar Creek Temperature
58 other water bodies Temperature

2020 Escherichia coli TMDL and Review

Five assessment units (four streams) within the South Fork Clearwater subbasin were identified as not supporting primary or secondary contact recreation beneficial uses due to exceedances of numeric E. coli criteria. TMDLs were developed to ensure primary or secondary contact recreation are protected for assessment units identified as impaired by E. coli. Additionally, a TMDL Five Year Review was completed on one assessment unit which recommend no changes to the previously approved E. coli TMDL on Three Mile Creek.

2020 TMDL: Streams and Pollutants for Which TMDLs were Developed

Stream Pollutants
Cottonwood Creek Escherichia coli
Stockney Creek Escherichia coli
Shebang Creek Escherichia coli
Sally Anne Creek Escherichia coli

Subbasin Document(s)

This accordion will not appear on the screen

DEQ Lewiston Regional Office
1118 F St.
Lewiston, ID 83501
Ph: (208) 799-4370
Fax: (208) 799-3451
Toll Free: (877) 541-3304

ver: 3.4.0 | last updated:
Jump back to top of page button