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Salmon River (Upper) Subbasin

Data Details
Hydrologic Unit Code 17060201
Size 2,425 square miles (1,552,000 acres)

Water Bodies with EPA-Approved TMDLs (Category 4a)

Challis Creek
Beneficial Uses Affected Domestic water supply, cold water aquatic life, salmonid spawning, primary and secondary contact recreation
Major Land Uses Forest, irrigated cropland, range, urban
Date Approved by EPA March 2003
Approval Letter
Date 2016 Addendum and Five-Year Review Approved by EPA December 2016
Approval Letter

Subbasin Characteristics

The Upper Salmon River subbasin is located in the central Idaho mountains. The mountainous terrain in this subbasin has produced many steep stream systems and glacial lakes and troughs that feed the headwaters of the Salmon River.

The waters of the upper Salmon River have been identified as an essential component of anadromous fish and Bull Trout restoration in Idaho. The Endangered Species Act requires that conservation plans be developed and implemented to restore anadromous fish and Bull Trout populations to levels that ensure their persistence in the Upper Salmon River subbasin.

2003 Subbasin Assessment and TMDL

Water quality, native fish populations, and riparian habitat conditions have been issues of concern in the Upper Salmon River subbasin. The cumulative effects of mining, grazing, over-utilization of riparian areas, timber harvest and associated roads, exotic species, residential and recreational development, and human-caused stream alteration and diversion have combined to limit the production and survival of native resident and anadromous fishes throughout the subbasin.

DEQ has identified Challis Creek as not fully supporting the beneficial uses of salmonid spawning and cold water biota. A TMDL for sediment has been prepared for this water body to restore full support of these beneficial uses. The Challis Creek TMDL should also assist in endangered species recovery.

Streams that already have best management practices in place that should result in attainment of water quality standards and beneficial use support in the near future do not require TMDLs. Streams that fall into this category are Thompson Creek and Kinnikinic Creek.

The two listed reaches of the Salmon River also do not require TMDLs because they fully support beneficial uses. A TMDL was also not prepared for Squaw Creek (listed for temperature), as it was found that the warm temperature in the creek is natural from geothermal sources.

Streams with flows less than 1 cubic foot per second are not held to narrative water quality standards. Lost Creek in the upper Stanley watershed is such a creek. It was listed in error and will not have a TMDL developed for it.

Challis Creek, Thompson Creek, and Yankee Fork are listed for flow and/or habitat alteration. It was also found that Garden, Warm Springs, and Road Creeks are impaired by flow alteration. However, the US Environmental Protection Agency 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.

2003 TMDL: Stream and Pollutant for Which TMDL Was Developed

Stream Pollutants
Challis Creek Sediment

2016 TMDL Addendum and Five-Year Review

This TMDL addendum and five-year review addresses the water bodies in the Upper Salmon River subbasin that have been placed in Category 5 of Idaho’s 2012 federally approved Integrated Report. In this document, each listed AU is examined. Temperature was determined to be impairing water quality in sixteen (16) AUs requiring temperature TMDLs: 8 listed in Category 5 of the 2012 Integrated Report and eight (8) unlisted but identified as having exceedances of the temperature standard for salmonid spawning. Temperature load allocations are provided in the document using the current Idaho Department of Environmental Quality (DEQ) methods for estimating shade. Sediment was found to be impairing beneficial uses in 4 AUs, and allocations for sediment load reductions are provided. In 1 AU, Escherichia coli (E. coli) was determined to be impairing water quality; a bacteria TMDL is provided for restoring the secondary contact recreation beneficial use to this AU. In total, 21 AUs received TMDLs.

The subbasin assessment portion examines water quality and use status for these AUs and summarizes completed or ongoing watershed improvement projects in the subbasin. The TMDL analyses quantify pollutant loads and allocate load reductions needed to return impaired waters to a condition meeting water quality standards. There are two individual NPDES permits for mine discharges (Hecla – Grouse Creek Unit and Thompson Creek Mine). These mines also have industrial stormwater general permits. There are potentially two aquaculture permits, a general permit for the state’s Sawtooth Fish Hatchery and a terminated individual permit for Epicenter Aquaculture. It is anticipated that the Epicenter facility will start up under new ownership and apply for an aquaculture general permit. This facility will discharge to a canal tributary to sediment TMDL waters and is receiving a wasteload allocation for its TSS load.

Effective target shade levels were established for sixteen (16) AUs (eight (8) listed and eight (8) unlisted) based on the concept of maximum shading under potential natural vegetation resulting in natural temperature levels. Shade targets were derived from effective shade curves developed for similar vegetation types in Idaho. Existing shade was determined from aerial photo interpretation or using the Oregon Department of Environmental Quality’s Heat Source modeling (shade-alator portion only). Estimates of existing shade were partially field verified with Solar Pathfinder data. Target and existing shade levels were compared to determine the amount of shade needed to bring water bodies into compliance with temperature criteria in Idaho’s water quality standards (IDAPA 58.01.02).

Idaho’s 2012 Integrated Report lists twelve (12) AUs for sediment-related impairments. Of these, eight (8) were found to be impaired for other causes (i.e., temperature or water withdrawals [Category 4c]) or were erroneously listed as impaired. The four (4) impaired AUs (all within the Warm Spring Creek watershed [5th field HUC—1706020115]) have TMDLs for sediment with allocations and reductions developed in this document (ID17060201SL131_04, SL132_02, SL132_03, and SL132_04).

No AUs were listed for bacteria impairment in the 2012 Integrated Report, either as fecal coliform or as E. coli. One unlisted AU required a bacteria TMDL for impairment to the recreation beneficial uses by E. coli. Herd Creek – source to mouth (ID17060201SL118_04) had a TMDL developed, along with load allocations and reductions.

2016 TMDL: Stream and Pollutant for Which TMDL Was Developed

Stream Pollutants
Salmon River Temperature
Challis Creek Temperature
Squaw Creek Temperature
Aspen Creek Temperature
Herd Creek E. coli
Warm Spring Creek Sediment

Subbasin Document(s)

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DEQ Idaho Falls Regional Office
900 N. Skyline Drive, Suite B
Idaho Falls, ID 83402
Ph: (208) 528-2650
Fax: (208) 528-2695
Toll Free: (800) 232-4635

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