Protecting Public Health and the Environment.

Clearwater River Subbasin

Subbasin at a Glance

Hydrologic Unit Code 17060306
Size 2,351 square miles (1,504,643 acres)

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

Big Bear Creek, Boulder Creek, Cedar Creek, Corral Creek, East Fork Potlatch Creek, Eldorado Creek, Grasshopper Creek, Hatwai Creek and tributaries, Heywood and Wilson Creeks and tributaries, Jim Brown Creek, Jim Ford Creek, Lapwai Creek, Lindsay Creek, Middle Potlatch Creek, Moose Creek, Musselshell Creek, Pine Creek, Potlatch River, Ruby Creek, West Fork Little Bear Creek, Winchester Lake, Winter Creek

Beneficial Uses Affected Cold water aquatic life, salmonid spawning, primary and secondary contact recreation, agricultural water supply, domestic water supply
Major Land Uses Farming, grazing, timber, recreation, urban, hydropower, small cattle operations, suburban, rangeland, industrial warehousing, road building, placer mining
Date Winchester Lake TMDL Approved by EPA March 1999
EPA Approval Letter
Date Jim Ford Creek TMDL Approved by EPA June 2000
EPA Approval Letter
Date Lindsay Creek TMDL Approved by EPA June 2007
EPA Approval Letter
Date Potlatch River TMDL Approved by EPA February 2009
Date Hatwai Creek TMDL Approved by EPA December 2010
EPA Approval Letter
Date Lolo Creek Tributaries TMDL Approved by EPA December 2011
EPA Approval Letter

Subbasin Characteristics

The Clearwater River subbasin is located in north-central Idaho, east of Lewiston. Much of the subbasin lies within the Nez Perce Reservation.

1999 Winchester Lake - Upper Lapwai Creek Watershed Assessment and TMDL

Watershed at a Glance

Winchester Lake and its watershed lie entirely within the Nez Perce Reservation in the Clearwater River subbasin. The lake sits approximately 30 miles southeast of Lewiston, Idaho, and 0.5 miles 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 also 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 tissue 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, 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.

1999 TMDL: Streams and Pollutants for Which TMDLs Were Developed

Winchester Lake
Nutrients, sediment
Upper Lapwai Creek
Nutrients, sediment, pathogens (bacteria), temperature

2000 Jim Ford Creek Watershed Assessment and TMDL

Watershed at a Glance

Jim Ford Creek is a 3rd-order tributary of the Clearwater River in the southern part of Clearwater County, Idaho. It drains a 65,838-acre watershed that has two distinct portions. In the upper portion, Jim Ford Creek flows through rolling forested uplands and the Weippe Prairie until it reaches the City of Weippe. Below Weippe, the creek enters a narrow, steep basalt canyon nearly 14 miles long. A 65-foot waterfall at the top of the canyon restricts fish passage upstream.

In 1994, Jim Ford Creek was classified as a high priority water quality limited segment under §303(d) of the Clean Water Act from its headwaters to its confluence with the Clearwater River. Grasshopper Creek, a tributary to Jim Ford Creek, was also classified as a water quality limited segment in 1994.

Three point sources are permitted to discharge in the Jim Ford Creek watershed. The primary nonpoint sources of pollutants in the Jim Ford Creek watershed are grazing, timber harvest activities, nonirrigated croplands, urban runoff, land development activities, and hydropower.

Existing data indicate fine sediment is not degrading the water quality of Jim Ford Creek; therefore, a TMDL was not written for fine sediment. However, a channel stability analysis and habitat survey indicated coarse sediment is impairing salmonid spawning and rearing in lower Jim Ford Creek, so a TMDL was developed for coarse sediment. A temperature TMDL was established to protect Chinook Salmon and steelhead spawning and other coldwater biota.

Visible nuisance algae growth and low dissolved oxygen levels indicate that Jim Ford Creek is impaired as a result of excess nutrients. Nuisance algae growths are present in the upper reaches of Jim Ford Creek, and low dissolved oxygen levels are present throughout the watershed. The nutrient and dissolved oxygen TMDLs were combined. An assumption was made that by meeting the instream nutrient target the dissolved oxygen water quality standard will also be achieved. A bacteria TMDL was written to protect primary contact recreation. Data indicated a TMDL for ammonia was not needed. The nutrient effects of ammonia were considered in the nutrient TMDL.

Limited sampling for oil and grease was conducted in 1998. None of the samples had a measurable amount of oil and grease. Given these results and because a regulatory framework exists to address oil and grease problems, a TMDL for oil and grease was not developed.

2000 TMDL: Subwatersheds and Pollutants for Which TMDLs Were Developed

Grasshopper Creek
Coarse sediment, temperature, total inorganic nitrogen, total phosphorus, bacteria
Heywood
Coarse sediment, temperature, total inorganic nitrogen, total phosphorus, bacteria
Jim Ford Creek
Coarse sediment, temperature, total inorganic nitrogen, total phosphorus
Jim Ford Creek (main stem)
Coarse sediment, temperature
Kamiah
Coarse sediment, temperature
Miles/Wilson
Coarse sediment, total inorganic nitrogen, total phosphorus, bacteria
Weippe (downstream)
Coarse sediment, temperature, total inorganic nitrogen, total phosphorus
Weippe (upstream)
Coarse sediment, total inorganic nitrogen, total phosphorus
Winter Creek
Coarse sediment, temperature, total inorganic nitrogen, total phosphorus, bacteria

2007 Lindsay Creek Watershed

Watershed at a Glance

Lindsay Creek is a 3rd-order tributary to the Clearwater River. The main stem of Lindsay Creek originates from springs at a wetland just below Mann's Reservoir and flows northwest to its confluence with the Clearwater River in Lewiston, Idaho.

DEQ established TMDLs to control bacteria, excess nutrients, and sediment in Lindsay Creek. Monitoring conducted in April 2005 indicates that a bacteria TMDL is needed to comply with Idaho water quality standards. A nutrient TMDL was developed to initiate protective ground water quality management actions, reduce nitrogen loading to the creek, and address the effects on the cold water aquatic life in the creek.

A sediment TMDL was developed to protect existing fish populations and restore habitat conditions in the watershed. The sediment TMDL allocates approximately 79% of the load capacity to nonpoint sources and provides a 3% wasteload allocation for potential inclusion into the City of Lewiston's future municipal National Pollutant Discharge Elimination System (NPDES) permit.

There are no known point sources that discharge to Lindsay Creek at this time. Nonpoint sources of bacteria in the Lindsay Creek watershed include livestock, septic systems, pets, and wildlife. In agricultural areas, fertilizers are a source of nutrients to subsurface waters and to Lindsay Creek through direct runoff. Manure from pets, wildlife, and livestock can contribute nutrients to the creek as well.

As a result of further water quality sampling and/or inconclusive data, it is recommended that temperature and dissolved oxygen be removed from the list of pollutants impairing Lindsay Creek and that no TMDLs be developed for these pollutants.

Since flow alteration and habitat alteration are not pollutants that can be quantified and allocated for loadings, TMDLs have not been developed for them.

2007 TMDL: Stream and Pollutants for Which TMDLs Were Developed

Lindsay Creek
Bacteria, nutrients, sediment

2008 Potlatch River Watershed Assessment and TMDL

Watershed at a Glance

The Potlatch River watershed, part of the Clearwater River subbasin, drains into the Clearwater River between Myrtle and Spalding. The upper reaches of the Potlatch River are divided into two main tributaries: the East Fork and West Fork Potlatch Rivers. The east fork originates in the northwest corner of Clearwater County and flows southwest to its confluence with the main stem. The west fork originates in the northwest corner of Latah County and flows southeast to its confluence with the Potlatch River. The Potlatch River drains the eastern two-thirds of Latah County, running from northeast to southwest.

Monitoring was conducted biweekly in 2002–2004. Water quality parameters and pollutant concentrations measured included stream temperature, E. coli and fecal coliform bacteria, dissolved oxygen, ammonia, total nitrogen and total phosphorus, turbidity and total suspended solids, pH, and streamflow. Based on data collected, DEQ is establishing TMDLs to control temperature, bacteria, excess nutrients, and sediment in various water body segments in the Potlatch River watershed.

TMDLs to restore stream temperatures to background conditions by increasing riparian shade were developed for all listed water bodies in the Potlatch River watershed. Temperature is a key factor in the quality of water bodies and the health of fish and other aquatic species.

Bacteria TMDLs were developed to control E. coli bacteria in several creeks. E. coli bacteria wasteload allocations also have been developed for five wastewater treatment facilities (Bovill, Deary, Juliaetta, Kendrick, and Troy) that discharge to the Potlatch River or associated tributaries and estuaries.

Nutrient TMDLs were developed to control excessive aquatic plant growth in Pine and West Fork Little Bear Creeks.

Lastly, sediment TMDLs were developed for several creeks. Wasteload allocations were developed for the Deary, Bovill, Kendrick, Juliaetta, and Troy wastewater treatment facilities based on the estimated design flow, the maximum daily limit, and the current allowable average monthly concentrations. Controlling sediment loads will assist in managing nutrient loads in the Potlatch River watershed since nutrients, particularly phosphorus, bind to soil particles delivered to the stream.

In addition, DEQ recommends removing various other pollutants from the list of pollutants associated with these water bodies because they are no longer impairing water quality.

A growth reserve is not included in the TMDLs. Except for stormwater construction permits, future sources will need to acquire a load allocation from existing allocations unless the load capacity is increased.

2008 TMDL: Streams and Pollutants for Which TMDLs Were Developed

Potlatch River (Big Bear Creek to Mouth)
Temperature, sediment
Potlatch River (Corral Creek to Big Bear Creek)
Temperature
Potlatch River (Moose Creek to Corral Creek)
Temperature
Potlatch River (Headwaters to Moose Creek)
Temperature, bacteria
Big Bear Creek
Temperature, bacteria
Boulder Creek
Temperature, bacteria
Cedar Creek
Temperature, sediment
Corral Creek
Temperature
Moose Creek
Temperature, bacteria
Pine Creek
Temperature, nutrients, sediment
Ruby Creek
Temperature, bacteria
East Fork Potlatch River
Temperature
Middle Potlatch Creek
Temperature, bacteria, sediment
West Fork Little Bear Creek
Bacteria, nutrients, sediment

2010 Hatwai Creek Watershed Assessment and TMDL

Watershed at a Glance

Hatwai Creek, a tributary of the Clearwater River, is located near the boundary between the Columbia Plateau and the Northern Rocky Mountains. The main stem of Hatwai Creek originates on the southern breaks of the Palouse Prairie, along the east side of Idaho State Highway 95, flowing south into a steep basalt canyon where it is fed by several springs before reaching the Clearwater River three miles east of Lewiston, Idaho.

During the TMDL investigation conducted by DEQ water quality analysts in summer 2006, bacteria, nutrients, and temperature were examined. Results for bacteria monitoring indicate that E. coli bacteria concentrations exceed water quality standards. Average nitrogen and total phosphorus concentrations also measured significantly higher than recommended. In addition, elevated temperatures were recorded as a result of removing riparian vegetation and replacing with agricultural crops, roads, and pasturelands. To address these pollutants, TMDLs have been developed to control excess bacteria, nutrients, and elevated temperature.

2010 TMDL: Stream and Pollutants for Which TMDLs Were Developed

Hatwai Creek
Bacteria, nutrients, temperature

2011 Lolo Creek Tributaries Watershed

Watershed at a Glance

Lolo Creek is a 6th-order tributary of the Clearwater River and forms the boundary between Idaho and Clearwater Counties in north-central Idaho. It flows primarily southwest, from just below the summit of Hemlock Butte to the Clearwater River near the town of Greer. A 24-mile stretch of Lolo Creek, from the mouth to the Clearwater National Forest boundary, flows through a steep, V-shaped canyon dominated by conifer forest, cliffs, rock outcrops, and talus slopes. The watershed above the canyon is comprised of open meadows interspersed with gently sloping, mostly forested upland. The subbasin is a sparsely populated area with no incorporated cities; much of the land is managed by federal and state agencies.

In the western portion of the watershed, major tributary drainages include Jim Brown Creek, which flows into Musselshell Creek; eastern portion tributary drainages include Yoosa and Eldorado Creeks. The major tributaries of the southern portion are Yakus and Crocker Creeks. Three main tributaries—Eldorado, Jim Brown, and Musselshell—show impairment and lack of support for their beneficial uses, which include cold water aquatic life, secondary contact recreation, and salmonid spawning, as a result of elevated temperatures. Temperature is a water quality factor integral to the lifecycle of fish and other aquatic species. TMDLs calling for more shade to reduce stream temperature have been developed.

It is anticipated that future restoration projects to address temperature will help reduce the amount of sediment, nutrients, and E. coli conveyed to the streams as well. As a result, the subbasin assessment recommends removing Eldorado and Musselshell Creeks from the state's list of impaired water bodies for unknown pollutants in the next Integrated Report and removing Jim Brown Creek for nutrients, sediment, and bacteria.

2011 TMDL: Streams and Pollutants for Which TMDLs Were Developed

Eldorado Creek
Temperature
Jim Brown Creek
Temperature
Musselshell Creek
Temperature

2017 Jim Ford Creek Temperature TMDL

Watershed at a Glance

Jim Ford Creek is a tributary of the Clearwater River in the southern part of Clearwater County. The creek drains a 65,838-acre watershed that has two distinct portions. In the upper portion, Jim Ford Creek flows through rolling forested uplands and the Weippe Prairie until it reaches the city of Weippe. Below Weippe, the creek enters a narrow, steep basalt canyon nearly 14 miles long. A 65-foot waterfall at the top of the canyon restricts fish passage upstream. The lower portion of Jim Ford Creek extends to the Nez Perce Tribal boundary.

The original 2000 Jim Ford Creek TMDL included temperature TMDLs for listed waters. These temperature TMDLs required revision to meet current methods. This 2017 TMDL revises the eight assessment units (AUs) in the Jim Ford Creek watershed that are in Category 4(a) of Idaho’s most recent Integrated Report for temperature impairment. An additional AU (ID17060306CL037_02) was originally listed for temperature in 1998 along with the other streams in this analysis, but was inadvertently left off the Category 4a list when AUs were created in the 2000s. That unit is being included now in the present TMDL analysis. All temperature TMDLs are being revised to the potential natural vegetation (PNV) style where riparian shade is the dominant influence on heat load to the stream. The TMDL analysis establishes water quality targets and load capacities, estimates existing pollutant loads, and allocates load reductions needed to return listed waters to a condition meeting water quality standards.

2017 TMDL: Streams and Pollutants for Which TMDLs Were Developed

Jim Ford Creek
Temperature
Grasshopper Creek
Temperature
Winter Creek
Temperature
Unnamed tributaries to Jim Ford Creek
Temperature

Subbasin Documents


Staff Contacts

Surface Water Quality Manager
Sujata Connell
DEQ Lewiston Regional Office
1118 "F" St.
Lewiston, ID 83501
(208) 799-4370
sujata.connell@deq.idaho.gov

Related Pages

Frequently Asked Questions about Subbasin Assessments and TMDLs

TMDL Implementation Plans

Table of Subbasin Assessments, TMDLs, Implementation Plans, and Five-Year Reviews