Water Quality Improvement Projects
Skagit Basin Area:


The Skagit River basin covers a about 2,730 square miles in Washington State and about 400 square miles in Canada. The river originates in British Columbia, flows through Ross Lake, past the town of Sedro Woolley, through Burlington and Mount Vernon, and after dividing into the North Fork and South Fork it empties into the Puget Sound at Skagit Bay.

The Skagit River is regulated by three hydroelectric dams: Gorge Dam at river mile (RM) 96.6, Diablo Dam at RM 101, and Ross Dam RM 105. The Skagit River provides hydroelectric power, drinking water, irrigation, fish and wildlife habitat, and extensive recreational opportunities. The area covered by this TMDL - the Lower Skagit River and its tributaries, and the North and South Fork Skagit River downstream to their mouths at Skagit Bay - is the lowland portion of the river downstream from the lower end of Skiyou Slough near Sedro-Woolley. The principal land uses in this area are agriculture, forestry and urban areas.

The Lower Skagit River, its tributaries, sloughs, and estuaries serve as important migration corridors, spawning areas, and rearing areas for five major species of salmon (chinook, coho, pink, chum, and sockeye), as well as steelhead and cutthroat trout, and two char species—Dolly Varden and bull trout. The Skagit River watershed contains the second largest wild run of coho salmon and the largest run of chinook salmon in the Puget Sound watershed. These salmonid species and other cold water aquatic life depend on the cool waters of smaller creeks in late summer for all or part of their life cycle.

Water quality issues

Fecal coliform

Up until 1991 the Skagit River was known to have good water quality and high flows. When WA Dept. of Health (WDOH) classified portions of the Skagit Bay shellfish beds as restricted or conditionally approved due to bacterial contamination, concerns were raised that the Skagit River's water quality may be impacting the resources of the bay. Limited data indicated that high fecal coliform bacteria in the lower Skagit River may contribute to problems in the Skagit Bay shellfish beds. Water quality in the sloughs and tributaries connected with the Skagit River were known to be poor as far back as 1975. A major water quality study in 1993 identified impairments for dissolved oxygen and fecal coliform, especially in the north and south forks, the sloughs, and in the Nookachamps system. The suspected sources were dairy farms, urban runoff, and failing septic systems. Based on this study the lower Skagit River basin was placed on Washington State's 303(d) list of polluted water bodies.


A Washington State Department of Ecology (Ecology) study, performed in August 2001, found that nine tributaries to Skagit River have elevated temperatures during the late summer, low-flow season. The affected creeks are Carpenter, Fisher, Hansen, Red, East Fork Nookachamps, Turner, Nookachamps, and Lake creeks, along with Otter Pond. The study determined that full, mature native riparian shade along these creeks may sufficiently reduce water heating so that the creeks meet the water quality temperature standard of 16o C, which is protective of spawning and juvenile rearing needs of salmon in those creeks.

Why this matters

Fecal coliform is a type of “bacteria” common in human and animal waste. It indicates that sewage or manure is entering a water body. As the level of fecal coliform increases, the risk of people getting sick from playing or working in the water increases. Bacteria can get into our waters from untreated or partially treated discharges from wastewater treatment plants, from improperly functioning septic systems, and from livestock, pets and wildlife.

People can help keep bacteria out of the water. Properly collect, bag, and trash dog poop. Check your on-site sewage system to make sure it is maintained and working properly. Ensure livestock and manure are kept away from the water.

Water temperature influences what types of organisms can live in a water body. Cooler water can hold more dissolved oxygen that fish and other aquatic life need to breathe. Warmer water holds less dissolved oxygen. Many fish need cold, clean water to survive.

One way to cool water temperature is to shade the water body by adding or retaining streamside vegetation.

Status of the project

Fecal coliform bacteria project

Ecology, along with local governments and special interest groups, developed a total maximum daily load (TMDL) for the Lower Skagit River. The TMDL determined wasteload allocations (WLAs) for dischargers covered by a national pollution discharge elimination system (NPDES) permit, and load allocations (LAs) for the part of the river upstream of Sedro-Woolley. The LAs also required the Nookachamps, Carpenter, and Fisher creeks to meet Class A water quality standards. The WLAs required all NPDES permitted dischargers to meet technology-based permit limitations, and abatement of combined sewer overflows (CSOs) to no more than one discharge per year.

Ecology submitted the final TMDL to EPA for approval. EPA approved the TMDL on September 1, 2000.

Lower Skagit tributaries temperature project

Ecology, assisted by a local advisory committee, developed a draft Water Quality Improvement Report (WQIR). The report describes Ecology's recommendations for reducing water temperatures in the nine affected creeks. It proposes a strategy of door-to-door outreach, education, and financial and technical assistance to private landowners to encourage them to increase riparian shading along these creeks.

Ecology submitted the final TMDL to EPA for approval. EPA approved the TMDL on August 11, 2008.

Technical information

Fecal coliform bacteria project

Unless stated otherwise, the following documents are Ecology publications.

Lower Skagit Total Maximum Daily Load Data Summary

Lower Skagit River Total Maximum Daily Load Water Quality Study

Lower Skagit River Fecal Coliform Total Maximum Daily Load Submittal Report -- Water Cleanup Plan

Lower Skagit River Fecal Coliform Total Maximum Daily Load: Water Quality Implementation Plan

Skagit Bay Fecal Coliform Bacteria Loading Assessment

Lower Skagit tributaries temperature project

Lower Skagit River Tributaries Temperature Total Maximum Daily Load Study

Lower Skagit Tributaries Temperature TMDL Water Quality Improvement Report

Related information

Unless stated otherwise, the following documents are Ecology publications.

Focus Sheet: Several creeks in the Lower Skagit watershed need your help

Focus on Temperatures in the Lower Skagit River Tributaries (2003)

WRIA 3: Lower Skagit-Samish Watershed Information (Water web site)


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Last updated March 2013
  Water resource inventory area (WRIA) 3 map, Washington State.


WRIA(s): #3 (Lower Skagit-Samish)
County:   Skagit

Water-body Names:
Skagit Basin
Tributaries of the Skagit River

Fecal coliform bacteria

# of TMDLs:
Fecal coliform bacteria - 8
Temperature - 8

Fecal Coliform - Approved by EPA
Has an implementation plan

Temperature - Approved by EPA

Contact Info:
Dave Garland
Phone: 425-649-7031
Email: Dave.Garland@ecy.wa.gov

Northwest Region
Department of Ecology
3190 - 160th Ave SE
Bellevue, WA 98008-5452