Stillaguamish River Watershed 

Fecal Coliform, Dissolved Oxygen, 

pH, Mercury, and Arsenic 

Total Maximum Daily Load 

(Water Cleanup Plan) 

Submittal Report 

April 2005 

Publication No. 05-10-044 
 
Stillaguamish River Watershed 

Fecal Coliform, Dissolved Oxygen, 

pH, Arsenic, and Mercury 

Total Maximum Daily Load 

(Water Cleanup Plan) 

Submittal Report 

Sally Lawrence and Joe Joy 

Washington State Department of Ecology 

Water Quality Program, Northwest Regional Office, Bellevue, 

and Environmental Assessment Program, Olympia, WA. 

April 2005 

Waterbody Numbers: (see Tables 8 & 9) 

Publication Number: 05-10-044 
This report is available on the Department of Ecology home page on the 

World Wide Web at http://www.ecy.wa.gov/biblio/05

This submittal report revises an earlier TMDL technical report published by Ecology in 

July 2004 and available on the World Wide Web at: 

http://www.ecy.wa.gov/biblio/0403017.html. 

For additional copies of this publication, please contact: 

Department of Ecology Publications Distributions Office 

Address: PO Box 47600, Olympia WA 98504-7600 

E-mail: ecypub@ecy.wa.gov 

Phone: (360) 407-7472 

Refer to Publication Number 05-10-044 

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Stillaguamish Bacteria and DO TMDL Submittal Report Page i 

Table of Contents 

 Page

List of Figures.................................................................................................................... iii 

List of Tables .......................................................................................................................v 

Definitions.......................................................................................................................... ix 

Executive Summary........................................................................................................... xi 

Introduction..........................................................................................................................1 

Background..........................................................................................................................5 

Setting ..............................................................................................................................5 

Flows..............................................................................................................................11 

Water Withdrawals ........................................................................................................15 

Potential Pollutant Sources ............................................................................................16 

Applicable Water Quality Criteria.....................................................................................21 

Water Quality and Resource Impairments.........................................................................25 

Beneficial Uses and Section 303(d) Listings.................................................................25 

Water Quality Assessments Since 1998 ........................................................................30 

Analytical Framework .......................................................................................................32 

Fecal Coliform ...............................................................................................................32 

Dissolved Oxygen..........................................................................................................35 

pH...................................................................................................................................39 

Arsenic and Mercury......................................................................................................40 

Seasonal Variation and Critical Conditions...................................................................40 

Technical Analysis.............................................................................................................41 

Flows and Rainfall .........................................................................................................44 

Fecal Coliform ...............................................................................................................47 

Dissolved Oxygen..........................................................................................................66 

pH...................................................................................................................................81 

Arsenic and Mercury......................................................................................................86 

Loading Capacity...............................................................................................................95 

Fecal Coliform ...............................................................................................................95 

Dissolved Oxygen........................................................................................................100 

pH.................................................................................................................................105 

Arsenic and Mercury....................................................................................................106 

Wasteload and Load Allocations .....................................................................................109 

Fecal Coliform .............................................................................................................109 

Dissolved Oxygen........................................................................................................112 

pH.................................................................................................................................114 

Arsenic and Mercury....................................................................................................115 

Margin of Safety ..............................................................................................................116 
Page ii Stillaguamish Bacteria and DO TMDL Submittal Report 

Summary Implementation Strategy .................................................................................117 

Implementation Overview ...........................................................................................117 

Implementation Plan Development..............................................................................119 

Approach for Non Point Sources .............................................................................120 

Approach for Point Sources.....................................................................................122 

Identified Needs and Early Action Proposals ..........................................................124 

Cost Estimates for Water Cleanup Projects.............................................................126 

Organizations with Programs to Improve Water Quality ........................................126 

Reasonable Assurances................................................................................................132 

Adaptive Management.................................................................................................133 

Monitoring Strategy.....................................................................................................134 

Recommendations for Monitoring...........................................................................135 

Initial Monitoring Needs..........................................................................................135 

Organizations that Monitor Water Quality ..............................................................136 

Potential Funding Sources ...........................................................................................137 

References Cited ..............................................................................................................138 

Appendix A. Public Participation Including Responses to Comments...................... A-145 

Appendix B. Wastewater Treatment Plants Point Sources – Descriptions.................B-155 

Appendix C. Monitoring Locations for Ecology July 2004 Technical Study ............C-171 

Appendix D. Equations and Examples of Calculations............................................. D-179 

Appendix E. Watershed Projects Already Implemented by Local Organizations......E-189 

Appendix F. NPDES Permitted Facilities in Stillaquamish Watershed .....................F-201

 
Stillaguamish Bacteria and DO TMDL Submittal Report Page iii 

List of Figures 

Figure 1. Generalized land cover in the study area........................................................................ 3 

Figure 2. Annual average precipitation in the Stillaguamish River watershed ............................. 7 

Figure 3. Surface hydrogeology of the Stillaguamish River watershed. ....................................... 8 

Figure 4. Land ownership in the Stillaguamish River watershed. ................................................. 9 

Figure 5. Flow gauging stations in the Stillaguamish River watershed....................................... 12 

Figure 6. A daily mean discharge hydrograph for the Stillaguamish River ................................ 13 

Figure 7. Locations of monitoring probes in the Stillaguamish River from Arlington to I-5...... 37 

Figure 8. Water quality monitoring sites used for storm-event and synoptic surveys................. 43 

Figure 9. Fecal coliform monitoring sites located in and around northern Port Susan.. ............. 44 

Figure 10. Estimated discharge record for the Stillaguamish River near Silvana . ..................... 47 

Figure 11. Bacteria count and loads collected at I-5 ................................................................... 50 

Figure 12. Ba teria statistical trends in the South Fork Stillaguamish River............................... 51 

Figure 13. Thirty sample running average bacteria counts at site PS-2, Port Susan. .................. 52 

Figure 14. Comparison of monthly median bacteria counts in Port Susan with 

estimated bacteria loads from the Stillaguamish River......................................................... 54 

Figure 15. Comparison of modeled bacteria counts with data for the lower 

Stillaguamish River .............................................................................................................. 57 

Figure 16. A box-plot summarizing monthly fecal coliform loads from data collected by 

Ecology at the Stillaguamish River at Interstate 5................................................................ 61 

Figure 17. Monthly dissolved oxygen measurements collected at Portage Creek at 

212th NE . .............................................................................................................................. 70 

Figure 18. Diel dissolved oxygen data recorded by probes deployed in the 

Stillaguamish River between Arlington and Interstate 5. ..................................................... 73 

Figure 19. Total phosphorus load in South Fork Stillaguamish River at Arlington, 

1979 to 2002 ........................................................................................................................ 76 

Figure 20. Simulations of maximum and minimum dissolved oxygen (DO) profiles in the 

mainstem Stillaguamish River.. ............................................................................................ 77 

Figure 21. Monthly pH statistics from the South Fork Stillaguamish River at Arlington .......... 82 

Figure 22. Total recoverable (TR) arsenic concentrations from samples collected at sites 

in the Stillaguamish River basin ........................................................................................... 89 

Figure 23. Correlations between total recoverable arsenic (TR Arsenic) and mercury (Hg) 

in whole water samples from four sites in the Stillaguamish River basin............................ 91 

Figure 24. Mercury concentrations for samples collected in the Stillaguamish River basin....... 92 
Page iv Stillaguamish Bacteria and DO TMDL Submittal Report 

Figure 25. Modeled dissolved oxygen concentrations in the Stillaguamish River from the 

confluence of the forks to Port Susan ................................................................................. 103 

Figure 26. Total phosphorus load trend in monthly data collected by Ecology at the 

North Fork Stillaguamish River ......................................................................................... 106 

Figure 27. Relationship between total suspended solids and mercury from sample sites 

on the mainstem Stillaguamish River. ................................................................................ 107 

Figure C-1. Sites in the lower river basin monitored for fecal coliform bacteria, 

dissolved oxygen and other conventional parameters. ................................................... C-175 

Figure C-2. Sites along mainstem of Stillaguamish River monitored for fecal coliform 

bacteria, dissolved oxygen, and other conventional parameters .................................... C-176 

Figure C-3. Sites along the North and South Forks of the Stillaguamish River monitored for 

fecal coliform bacteria, dissolved oxygen, pH, and other conventional parameters ..... C-177
Stillaguamish Bacteria and DO TMDL Submittal Report Page v 

List of Tables 

Table ES-1. Summary of Loading Capacity and Wasteload and Load Allocations for 

Stillaguamish Reaches ......................................................................................................... xiv 

Table ES-2. Recommended Fecal Coliform Limits and Wasteload Allocations for Three 

Wastewater Treatment Plants with NPDES Permits ........................................................... xvi 

Table ES-3. Summary of Loading Capacity and Wasteload and Load Allocations for 

Stillaguamish Reaches with Fecal Coliform Impairments.................................................. xvii 

Table ES-4. Load Allocations for Stillaguamish Reaches with pH Impairments......................... xx 

Table ES-5. Load Allocations for Stillaguamish Reaches with Mercury Impairments................ xx 

Table 1. Stillaguamish River basin (Water Resource Inventory Area 5) and Port Susan 

(WRIA 6) water bodies on the 1998 Section 303(d) list for TMDL evaluations. .................. 2 

Table 2. Mean daily discharge (in cfs) by month for two long-term USGS gage stations 

on the North Fork and South Fork Stillaguamish River. ...................................................... 13 

Table 3. Summary of the annual 7-day, 10-year (7Q10), low-flow statistics for USGS 

gauging stations in the Stillaguamish River basin. ............................................................... 15 

Table 4. Summary of consumptive water rights in the Stillaguamish River watershed.............. 16 

Table 5. Bird population data for northeast Port Susan, Livingston Bay, and the 

Stillaguamish River delta...................................................................................................... 20 

Table 6. Current state water quality and National Toxics Rule criteria used to determine if 

Stillaguamish River basin waters and Port Susan are supporting beneficial uses ................ 22 

Table 7. Recommended EPA nutrient criteria for Level III ecoregions, Puget Sound and 

North Cascades, in aggregate Ecoregion II (EPA, 2000). .................................................... 24 

Table 8. Stillaguamish River basin water bodies on the 1996 and/or 1998 Section 303(d) 

list for fecal coliform bacteria, dissolved oxygen, arsenic or pH ......................................... 27 

Table 9. Stillaguamish Basin water bodies previously unlisted but found through TMDL 

to be impaired. ...................................................................................................................... 28 

Table 10. General timing of life-stages of Stillaguamish basin salmon species.......................... 29 

Table 11. Flow statistics for the North Fork Stillaguamish River near Arlington comparing 

period of record data to water years 2000 and 2001............................................................. 45 
Page vi Stillaguamish Bacteria and DO TMDL Submittal Report 

Table 12. Fecal coliform statistics calculated for 30 consecutive samples collected by the 

Stillaguamish Tribe prior to June 27, 2002 at 16 sites.......................................................... 53 

Table 13. Fecal coliform results from samples collected from freshwater and 

marine waters in and around northern Port Susan . ............................................................. 55 

Table 14. Fecal coliform results at selected sites in the Stillaguamish River basin for samples 

collected during two, 2-day storm-event surveys in 2001. ................................................... 58 

Table 15. Statistical summary of fecal coliform samples collected weekly from seven 

beach sites in the Stillaguamish River basin......................................................................... 60 

Table 16. Bird population data for northeast Port Susan, Livingston Bay, and the 

Stillaguamish River delta, and estimates of the daily fecal coliform load............................ 62 

Table 17. Statistical summaries of fecal coliform samples collected from sites in the 

Stillaguamish River basin during this TMDL daily load study ............................................ 64 

Table 18. A summary of dissolved oxygen concentrations from grab samples collected 

in the Stillaguamish River basin. ......................................................................................... 67 

Table 19. Comparison of key characteristics during three diel dissolved oxygen (DO) 

surveys on the Stillaguamish River below Arlington. .......................................................... 74 

Table 20. Headwater, point source, and tributary input values used to evaluate Stillaguamish 

River dissolved oxygen in the model simulations under critical low-flow conditions......... 79 

Table 21. Summary of instantaneous pH measurements made in the Stillaguamish 

River basin. ........................................................................................................................... 83 

Table 22. Total recoverable and dissolved arsenic concentrations and total suspended solids 

concentrations collected from sites on the Stillaguamish River. .......................................... 86 

Table 23. Total recoverable arsenic (TR As), total suspended solids (TSS), and 

flow data at two sites in the Stillaguamish River basin. ....................................................... 87 

Table 24. Total recoverable mercury concentrations from sites on the Stillaguamish River ..... 90 

Table 25. Quarterly mercury, total suspended solids, and discharge data collected in 

2002 from North Fork Stillaguamish River near Darrington............................................... 92 

Table 26. Fecal coliform statistical summaries for freshwater monitoring sites along the 

mainstem Stillaguamish River and major forks and tributaries............................................ 96 

Table 27. Fecal coliform critical condition summaries for tributaries to the Old Stillaguamish 

Channel near Stanwood. ....................................................................................................... 97 
Stillaguamish Bacteria and DO TMDL Submittal Report Page vii 

Table 28. Fecal coliform critical condition summary for West Pass, South Pass, and small 

tributaries to Port Susan........................................................................................................ 97 

Table 29. Estimated average daily fecal coliform loads to Port Susan from various 

sources for the months of June through December............................................................... 98 

Table 30. Fecal coliform target geometric means calculated from statistics derived for 30 

consecutive samples collected by the Stillaguamish Tribe prior to June 27, 2002............... 99 

Table 31. Dissolved oxygen minimum concentrations estimated for reaches in the 

Stillaguamish River basin based on considerations of local natural and pollutant sources.101 

Table 32. Summary of simulations of Arlington WWTP input and Stillaguamish River 

minimum dissolved oxygen responses during critical low-flow conditions....................... 103 

Table 33. Stillaguamish River basin and Port Susan tributaries listed in Section 303(d) 

in 1998. ............................................................................................................................. 109 

Table 34. Additional Stillaguamish River basin and Port Susan tributaries not listed in 

Section 303(d) in 1998........................................................................................................ 110 

Table 35. Fecal coliform (FC) wasteload allocations for stormwater discharge permit 

holders, Snohomish County and the Washington State Department of Transportation. .... 111 

Table 36. Recommended fecal coliform limits and wasteload allocations (WLA) for three 

wastewater treatment plants with NPDES permits. ............................................................ 112 

Table 37. Estimates of the BOD5 loading capacities, load allocations (LA), and wasteload 

allocations (WLA) for six sites in the Stillaguamish River basin....................................... 113 

Table 38. Load allocations for Total Phosphorus in the North Fork Stillaguamish River 

to reduce periphyton biomass and address elevated pH measurements. ............................ 115 

Table 39. Preliminary Proposals for Improving Water Quality.................................................. 125 

Table 40. Schedule for Detailed Implementation Plan (DIP) and Adaptive Management........ 134 

Table B1. Arlington NPDES permit limits............................................................................ B-157 

Table B2. Indian Ridge Corrections Center NPDES permit limits ....................................... B-158 

Table B3. Warm Beach Conference Center NPDES permit limits, interim.......................... B-159 

Table B4. Warm Beach Conference Center NPDES permit limits, final .............................. B-159 

Table B5. Twin City Foods State Waste Discharge permit limits......................................... B-161
Page viii Stillaguamish Bacteria and DO TMDL Submittal Report 

Table B-6. Fecal Coliform Data Used to Determine Arlington WWTP Permit Limits ........ B-161 

Table B-7. Fecal Coliform Data Used for Permit Limit Calculations for Indian Ridge 

Corrections Facility......................................................................................................... B-164 

Table B-8. Fecal Coliform Data Used to Determine Warm Beach WWTP Permit Limits.... B-166 

Table B-9. Fecal Coliform Data Used to Determine WWTP Permit Limits.......................... B-167 

Table C-1. Locations of monitoring stations. ........................................................................ C-173 

Table D1. Mean concentration estimates and percent imperviousness for various 

land uses.......................................................................................................................... D-185 

Table D2. Land use assumptions for individual sub-basins as percentages. ......................... D-185 

Table D-3. Example of Wasteload Allocation Calculation for BOD ..................................... D-186 

Table E-1. Recent City of Arlington Projects Addressing Impaired Waters in 

Stillaguamish Watershed .................................................................................................E-191 

Table E-2. 2002-2004 Stillaguamish BankSavers Riparian Planting in 

Stillaguamish Watershed (Stillaguamish Tribe) ..............................................................E-196 

Table E-3. Portage Creek Watershed Revegetation Sites - The BankSavers Project 

(Stillaguamish Tribe) .......................................................................................................E-197 

Table E-4. Recent Snohomish County/Partner Projects Addressing Impaired Waters in 

Stillaguamish Watershed .................................................................................................E-198 

Table E-5. Snohomish Conservation District: 2004 Public Education Projects in 

Stillaguamish Watershed .................................................................................................E-199 

Table E-6. Snohomish Conservation District: 2004 Projects in Stillaguamish Watershed ....E-199 

Table F-1. NPDES permitted facilities in Stillaguamish Basin with active 

permits that discharge directly to surface water. .............................................................F-203 
Stillaguamish Bacteria and DO TMDL Submittal Report Page ix 

Definitions 

303(d) list: § 303(d) of Clean Water Act requires states to establish a list of water bodies that do 

not meet water quality standards. Now called the Washington State Water Quality Assessment. 

Background (Natural Bckground Levels): Surface water quality that was present before any 

human-caused pollution (WAC 173-201A). 

Best Management Practices (BMPs): The schedules of activities, prohibitions of practices, 

maintenance procedures, and structural and/or managerial practices, that when used singly or in 

combination, prevent or reduce the release of pollutants and other adverse impacts to waters of 

Washington State.

Clean Water Act (CWA): Federal Act passed in 1972 that contains provisions to restore and 

maintain the quality of the nation’s waters. § 303(d) establishes the TMDL program. 

Fecal Coliform (FC): Bacteria present in intestinal tracts and feces of warm-blooded animals. 

FC are “indicator” organisms that suggest the possible presence of disease-carrying organisms. 

Concentrations are measured in colony-forming units per 100 milliliters of water (cfu/100mL). 

Geometric Mean: Like the arithmetic mean, mode and median, an “average” that can be 

calculated for a set of values. The geometric mean is the antilogarithm of the arithmetic mean of 

the logarithms of the individual sample values. Commonly reported for fecal coliform data. 

Hyporheic Zone: The volume of saturated sediment beneath and beside streams and rivers 

where ground water and surface water mix. 

Load Allocation (LA): The portion of a receiving waters’ loading capacity attributed to one of 

its existing or future nonpoint sources of pollution or to natural background sources. 

Loading Capacity: The greatest amount of contaminant loading that a water body can receive 

and still meet water quality standards. 

Municipal Separate Storm Sewer Systems (MS4): A system of pipes, ditches, or other 

stormwater conveyances under the jurisdiction of a municipality (such as Snohomish County and 

Washington State Department of Transportation). 

National Pollutant Discharge Elimination System (NPDES): National program for issuing, 

modifying, revoking, reissuing, terminating, monitoring and enforcing permits, and imposing 

and enforcing pretreatment requirements under the Clean Water Act. 

Nonpoint Source: Generally any unconfined and diffuse source of contamination, such as 

stormwater or snowmelt runoff or atmospheric pollution. Legally, any source of water pollution 

that does not meet the legal definition of “point source” in §502(14) of the Clean Water Act. 

90th percentile: An estimated portion of a sample population based on a statistical 

determination of distribution characteristics. The 90th percentile value is a statistically derived 
Page x Stillaguamish Bacteria and DO TMDL Submittal Report 

estimate of the division between 90 percent of samples, which should be less than the value, and 

10 percent of samples, which are expected to exceed the value. 

Pathogen: Disease-causing microorganisms such as bacteria, protozoa, viruses. 

Phase I Stormwater Permit: The first phase of stormwater regulation required under the 

federal Clean Water Act covering medium and large municipal separate storm sewer systems and 

construction sites of five or more acres. 

Phase II Stormwater Permit: The second phase of stormwater regulation required under the 

Clean Water Act covering smaller municipal separate storm sewer systems (MS4s) and 

construction sites over one acre. 

Point Source: Sources of pollution that discharge at a specific location from pipes, outfalls, and 

conveyance channels from either municipal wastewater treatment plants, municipal stormwater 

facilities, or industrial waste treatment facilities. Point sources can also include pollutant loads 

contributed by tributaries to main receiving water body. 

Pollution: Contamination or other alteration of the physical, chemical or biological properties of 

waters of the state; including change in temperature, taste, color, turbidity or odor of the waters, 

or such discharge of any liquid, gaseous, solid, radioactive, or other substance into any waters of 

the state that is likely to create a nuisance or render such waters harmful, detrimental, or 

injurious to the public health, safety, and welfare; or to domestic, commercial, industrial, 

agricultural, recreational, or other legitimate beneficial uses, or to livestock, wild animals, birds, 

fish, or other aquatic life. 

Pollution Identification and Correction (PIC) Project: Water quality improvement project 

focused on a single sub watershed developed by Kitsap Health District to address fecal coliform 

contamination in streams. Involves public outreach, detailed water quality monitoring, source 

identification and correction under Kitsap County regulatory programs. 

Stormwater: Water that runs off roads, pavement, and roofs during rainfall or snow melt; can 

also come from hard or saturated grass surfaces such as lawns, pastures, playfields, and from 

gravel roads and parking lots. 

Total Maximum Daily Load (TMDL): The amount of a pollutant that a stream, lake, estuary, 

or other water body can accept without violating state water quality standards. TMDLs can be 

expressed in terms of mass per time, toxicity, or other appropriate measures that relate to a 

state’s water quality standard. 

Wasteload Allocation (WLA): The portion of a receiving water’s loading capacity allocated to 

one of its existing or future point sources of pollution and covered by the NPDES Program. 

WLAs constitute a type of water quality-based effluent limitation. 

Watershed: A drainage area or basin in which all land and water areas drain or flow toward a 

central collector such as a stream, river, or lake at a lower elevation. 
Stillaguamish Bacteria and DO TMDL Submittal Report Page xi 

Executive Summary 

The total maximum daily load (TMDL) for the Stillaguamish River watershed and Port Susan in 

Snohomish County, Washington addresses water quality impairments for fecal coliform bacteria, 

dissolved oxygen, pH, arsenic, and mercury. Washington Department of Ecology (Ecology) has 

determined loading capacity and established load allocations and wasteload allocations 

(summarized in Tables ES-1 through ES-5) for the impaired water bodies in accordance with 

state water quality regulations and in accordance with Ecology’s 1997 Memorandum of 

Agreement with U.S. Environmental Protection Agency. 

Recreational and commercial shellfish harvesting are the beneficial uses to be protected by 

reducing fecal coliform loading to Port Susan marine waters. The load reductions needed to 

protect these beneficial uses are established through load and wasteload allocations for a number 

of different point and nonpoint sources. At present, Port Susan waters do not meet state 

Department of Health criteria for commercial shellfish harvest. Freshwater and nearshore 

marine primary and secondary contact recreational uses will also be protected with these 

allocations, and the health of aquatic life will be protected by allocations addressing pH, 

dissolved oxygen, and mercury impairments. 

The waters of Port Susan, the mainstem Stillaguamish River, its major forks and a number of 

tributaries and smaller creeks are impaired with excess fecal coliform bacteria. This analysis 

identified seasonal critical conditions that varied with location but most often included both 

summer dry and fall rainy periods, approximately June through December. The Statistical 

Rollback Method was used to determine the bacteria reductions needed for each impaired reach 

to meet water quality standards. A total of 34 water bodies or stream reaches require reductions 

in bacteria. Reaches requiring the greatest reductions (90 percent or more) are Glade Bekken 

Creek, Lake Martha Creek, Unnamed Creek #456 in the Warm Beach residential area, March 

Creek, and Warm Beach Dike Pond. 

Although many of the fecal coliform impairments result from non-point pollution, some stream 

reaches are likely affected by stormwater runoff from municipalities that have NPDES Phase I 

stormwater permits or that will be covered by the future NPDES Phase II permit. Based on 

guidance from EPA (Wayland and Hanlon, 2002), these municipalities are given wasteload 

allocations for fecal coliform bacteria in this TMDL. According to the EPA guidance, the 

wasteload allocations for stormwater will typically be reflected in the stormwater permits not as 

numeric effluent limits but as Best Management Practices (BMPs). 

The waters of Portage Creek, Pilchuck Creek, mainstem Stillaguamish below Arlington, March 

Creek, Kackman Creek, Warm Beach Creek, and Dike Pond are impaired at times with 

insufficient dissolved oxgyen. Seasonal critical conditions for dissolved oxygen occur during 

late summer and early fall low-flow periods. For all water bodies except the mainstem, current 

point and nonpoint loading of oxygen-consuming organic matter (biochemical oxygen demand, 

or BOD) delivered from various land uses was estimated using the Simple Method Model for 

estimating urban stormwater loads. Load and wasteload allocations were established by 

apportioning the loading capacities accordingly. Two local jurisdictions (Snohomish County and 
Page xii Stillaguamish Bacteria and DO TMDL Submittal Report 

city of Arlington) and a state agency (Washington State Department of Transportation) are 

allocated wasteloads for BOD that will be referenced in their NPDES stormwater permits. As 

cited above, the EPA guidance states that rather than establishing numeric effluent limits, the 

stormwater permits will most frequently specify BMPs that would reduce stormwater 

contributions of BOD to the receiving waters. 

 

The dissolved oxygen (DO) impairment of the mainstem Stillaguamish below Arlington may 

result from a combination of point and nonpoint-source nutrient inputs that lead to periphyton 

growth (with associated oxygen-consuming impacts at night and organic decay). The low DO at 

this location may also be influenced by inflows of low-DO ground water. The QUAL2Kw water 

quality model was used to attempt to determine relative roles of nonpoint and point sources 

(including Arlington’s wastewater treatment plant); however, the results were not definitive and 

no load allocations or wasteload allocations were set for this reach. Additional monitoring is 

recommended. 

The loading capacities for fecal coliform bacteria resulted in recommended reduced fecal 

coliform permit limits (compared with current permits) for Arlington Wastewater Treatment 

Plant (WWTP) and Warm Beach Conference Center WWTP. No change was required for the 

Indian Ridge Corrections Center WWTP. However, the additional requirement that Warm 

Beach Conference Center WWTP discharge zero BOD to the small creek to which it currently 

discharges effectively requires the Conference Center to find a different effluent discharge 

location. 

For pH, the South Fork Stillaguamish reach at Arlington that was listed on the 1998 303(d) list is 

recommended for delisting. Additional monitoring is recommended for Pilchuck, Kackman, and 

March Creeks (none of these currently listed for pH) to assess status for future potential listings. 

A load allocation for phosphorus is established for the North Fork to limit conditions that favor 

periphyton growth associated with high pH. 

Both arsenic and mercury in this watershed are associated with natural geologic sources without 

enrichment from anthropogenic sources. Higher concentrations in water samples are associated 

with elevated suspended solids which have many sources including natural erosion areas. 

Arsenic concentrations are consistently above the 0.14 ug/L EPA human health drinking water 

criterion for a 1 in 1 million cancer risk, but are much lower than aquatic toxicity criteria. Sites 

in the Stillaguamish watershed were included in an Ecology 2002 statewide study of arsenic 

concentrations in rivers. The study recommends that most 303(d) listings for arsenic across the 

state be removed and that future listings define an anthropogenic source. The one 1998 303(d) 

listing for arsenic in the mainstem Stillaguamish is recommended for delisting. 

Mercury concentrations did occur above the chronic aquatic toxicity criterion during two 

moderately high-flow events. Reducing total suspended solids, especially TSS mobilized during 

storm events, would reduce mercury transport and availability. This evaluation establishes a 

load allocation for TSS in order to reduce the occurrence of mercury concentrations at levels 

higher than the chronic aquatic toxicity criterion. 
Stillaguamish Bacteria and DO TMDL Submittal Report Page xiii 

A number of conservative assumptions were made during TMDL analyses, which provide the 

required Margin of Safety for the analysis. 

This TMDL includes a Summary implementaion strategy to guide implementation of water 

cleanup programs and actions to restore these impaired waters. Implementing agencies and 

organizations in the watershed will use existing regulations and programs to reduce high bacteria 

concentrations, address dissolved oxygen deficits and pH excursions, and reduce mercury 

concentrations. The wasteload allocations for wastewater treatment plants and jurisdictions with 

NPDES municipal separate stormwater permits will be referenced as requirements in the next reissuance of these NPDES permits. For the wastewater treatment plants, the requirements will be 

in the form of effluent discharge limits, however, for the stormwater permittees, the requirements 

will likely be in the form of Best Management Practices. 

Among new local programs that will help meet this TMDL’s goals are a funding initiative by 

Snohomish County to increase the local health district’s capability to investigate potential septic 

system failures; the Stillaguamish Tribe’s initiative to acquire sufficient funds to redirect the 

course of the North Fork around the toe of the Steelhead Haven landslide, thus reducing 

sediment inputs; and ongoing riparian restoration programs by the city of Arlington; the StillySnohomish Fisheries Enhancement Group, the Stillaguamish Tribe, and the Snohomish County 

Stillaguamish Steward. 

Ecology will make Centennial Clean Water Fund grant monies available for competitive 

Stillaguamish Basin restoration and water quality related projects and will award extra ranking 

points for projects that help implement approved TMDLs. 

Ecology will provide organizational support for local efforts through an annual review of water 

quality monitoring results and by following an adaptive management strategy to evaluate and 

redirect implementation measures as appropriate. Ecology will also use its authority under 

Chapter 90.48 RCW to enforce water quality regulations whenever applicable best management 

practices are not being implemented and Ecology has reason to believe that individual sites or 

facilities are causing pollution. 

It is estimated that it will take eight years for the projects and programs developed under the 

implementation plan to result in measurable progress in water quality, so the target date for this 

TMDL is 2013. 
Page xiv Stillaguamish Bacteria and DO TM

Table ES-1. Summary of Loading Capacity and Wasteload and Load Allocations for Stillaguamish Reaches with both Fecal Coliform and Dissolved Oxygen Impairments 

Water Body WBID Parameter 

Current 

Load 

(cfu/day) 

Loading Capacity:

Target Geometric Mean 

(cfu) or Estimated 

Potential Minimum 

Dissolved Oxygen 

(mg/L) 

(or BOD in lb/day) 

Total % 

Reduction 

Required 

Percent of 

Load 

(estimate) 

Was

or L

Allo

19 3.6 

0.4 7.5 1.2 2.2 

Fecal Coliform 9.35 x 1010 10 cfu/100 mL 98 

79.4 1.5 

2 (0

0.1 (00.2 (0

33 (

March Creek WI88QF 

Dissolved Oxygen 

(BOD5 in lb/day) 

6.5 mg/L 

(31) 

66 (2

3.6 2.1 

Fecal Coliform 1.79 x 10 

10 33 cfu/100 mL 68 

96.4 5.5 

6 (0

50 (

Kackman Creek 

at 252nd XB43NX 

Dissolved Oxygen 

(BOD5 in lb/day) 

7 mg/L 

(10) 

40 (

2.9 2.0 1.8 1.3 

Fecal Coliform 4.16 x 1011 25 cfu/100 mL 83 

95.3 6.7 

4 (

3 (

70 (2

Portage Creek at 

212th NE OT80TY 

Dissolved Oxygen 

(BOD5 in lb/day) 

6.5 mg/L 

(300) 

23 (
Stillaguamish Bacteria and DO TMDL Submittal Report 

Table ES-1 (continued). Summary of Loading Capacity and Wasteload and Load Allocations for Stillaguamish Reaches with both Fecal Coliform and Dissolved Oxygen Impairments 

Water Body WBID Parameter Current 

Load 

(cfu/day) 

Loading Capacity:

Target Geometric Mean 

(cfu) or Estimated 

Potential Min. 

Dissolved Oxygen 

(mg/L) 

(or BOD in lb/day) 

Total % 

Reduction 

Required 

Percent of 

Load 

(estimate) 

Was

or L

Allo

39 4.4 

Fecal Coliform 3.69 x 10 

11 45 cfu/100 mL 69 

61 7.0 

57 (140 (1

Portage Creek at 

43rd NE 

OT80TY 

Dissolved Oxygen 

(BOD5 in lb/day) 

 7 mg/L 

(250) 

3 (

2.5 9.0 

16.5 6.0 

Fecal Coliform 4.89 x 1011 38 cfu/100 mL 26 

81 2.9 

3 (2

20 (139 (3

Pilchuck Creek at 

Jackson Gulch Rd 

VJ74AO 

Dissolved Oxygen 

(BOD5 in lb/day) 

 8 mg/L 

(890) 

37 (3

Fecal Coliform 3.11 x 1010 47 cfu/100 mL 81 100 5.9 

7 (10 (

Warm Beach 

Creek above 

WWTP 

SH96KX 

Dissolved Oxygen 

(BOD5 in lb/day) 

 8 mg/L 

(20) 

93 (1
Page xvi Stillaguamish Bacteria and DO TM

Table ES-1 (continued). Summary of Loading Capacity and Wasteload and Load Allocations for Stillaguamish Reaches with both Fecal Coliform and Dissolved Oxygen Impairments 

Water Body WBID Parameter Current 

Load 

(cfu/day) 

Loading Capacity:

Target Geometric Mean 

(cfu) or Estimated 

Potential Minimum 

Dissolved Oxygen 

(mg/L) 

(or BOD in lb/day) 

Total % 

Reduction 

Required 

Percent of 

Load 

(estimate) 

Was

or 

Allo

4.3 1.5 

Fecal Coliform 4.23 x 1010 14 cfu/100 mL 92 

95.7 3.2 

5 (1

67 (

Warm Beach 

Dike Pond 

(includes BOD 

loading from 

Warm Beach 

Creek, above) 

SH96KX 

Dissolved Oxygen 

(BOD5 in lb/day) 

 6.5 mg/L 

(30) 

27 

*Load allocation of 1.4 lb BOD/day for Snohomish County carried from entry above for Warm Beach Creek 

Table ES-2. Recommended Fecal Coliform Limits and Wasteload Allocations for Three Wastewater Trea

with NPDES Permits 

Current FC Permit Proposed Permit Facility Name cfu/100 mL cfu/100 mL 

Indian Ridge Corrections Center WWTP 100 100 Arlington WWTP 200 / 400 39 / 128 Warm Beach Conference Center WWTP* 200 / 400 47 / 100 Warm Beach Conference Center WWTP** - 11 / 26 

* Assuming discharge to Warm Beach Creek at current maximum monthly flow of 0.075 MGD, and the discharge is allowed un

** Assuming discharge to Hat Slough near the South Branch with maximum monthly flow of 0.075 MGD. 
Stillaguamish Bacteria and DO TMDL Submittal Report 

Table ES-3. Summary of Loading Capacity and Wasteload and Load Allocations for Stillaguamish Reaches with Fecal Coliform Impairments A. Port Susan and Discharges to Port Susan 

Water Body WBID Current 

Bacteria Load 

(cfu/day) 

Loading Capacity: 

Target Geometric 

Mean (cfu/100 

mL) 

Total Percent 

Reduction 

Required 

Percent of 

Load 

(estimate) 

Wasteload 

or Load 

Allocation 

Port Susan 390KRD Note 1 14 61 100 Note 1 

6.9 1.1 x 108 Unnamed Creek #0456 LU17DC 5.17 x 10 

10 11 97 

93.1 1.4 x 109 

8.8 4.5 x 108 Lake Martha Creek IJ55EP 6.38 x 10 

10 23 92 

91.2 4.6 x 109 

Warm Beach Slough IE90YH Note 1 10 64 100 Note 1 

Agricultural Drain to 

Warm Beach Dike Pond 

SH96KX 8.86 x 109 13 89 100 9.8 x 108 

Twin City Foods Drain #4 WC93GU Note 1 18 88 100 Note 1 

West Pass of Old 

Stillaguamish Channel 

XF13JD 6.1 x 1010 3 97 100 9.0 x 108 

South Pass of Old 

Stillaguamish Channel 

UJ01AO 2.45 x 1011 11 75 100 6.1 x 1010 

Hat Slough (Stillaguamish 

River) at Marine Drive 

ZO73WL 5.79 x 1012 36 36 100 3.71 x 1012 

Note 1: Insufficient data to calculate load 
Page xviii Stillaguamish Bacteria and DO TM

Table ES-3. Summary of Loading Capacity and Wasteload and Load Allocations for Stillaguamish Reaches with Fecal Coliform Impairments B. Old Stillaguamish Channel Tributaries* 

Water Body WBID Critical Condition 

Geometric 

Mean (cfu/100 

mL) 

Loading Capacity: 

Target Geometric 

Mean (cfu/100 mL) 

Total Percent 

Reduction 

Required 

Percent of 

Load 

(estimate) 

N

Douglas Slough AS64WF 40 13 68 100 

Irvine Slough HS19KT 730 7 99 100 

Jorgenson Slough 

(lower Church Creek) GH05SX 320 42 87 100 

Church Creek at Park GH05SX 147 38 74 100 

Miller Creek at Miller Rd KX60NO 311 28 91 100 

Twin City Foods Drain #1 JV77EY 406 24 94 100 Twin City Foods Drain #2 JV77EY 285 3 99 100 Twin City Foods Drain #3 JV77EY 1180 24 98 100 Twin City Foods Drain #5 JV77EY 545 22 96 100 

* Discharges (flows) and fecal coliform loads will be calculated during development of the Old Stillaguamish Channel TMDL 

fall 2006. Because measurements of fecal coliform concentration made in 2001 (during sampling for this Stillaguamish TMD

coliform reductions are recommended to support immediate cleanup planning and implementation. 
Stillaguamish Bacteria and DO TMDL Submittal Report 

Table ES-3. Summary of Loading Capacity and Wasteload and Load Allocations for Stillaguamish Reaches with Fecal Coliform Impairments C. Stillaguamish Mainstem and Tributaries Below Arlington 

Water Body WBID Current 

Bacteria 

Load 

(cfu/day) 

Loading Capacity: 

Target Geometric 

Mean (cfu/100 

mL) 

Total 

Percent 

Reduction 

Required 

Percent of 

Load 

(estimate) 

Wasteload 

or Load 

Allocation 

6.5 3.9 x 108 Glade Bekken FJ67XF 7.42 x 10 

10 18 92 

93.5 5.5 x 109 

Stillaguamish River at I-5 QE93BW 6.27 x 1012 26 52 100 3.0 x 1012 

5 7.0 x 108 Fish Creek QJ28UC 7.4 x 10 

10 32 81 

95 1.3 x 1010 

2.3 1.6 x 109 1.2 8.6 x 108 

Armstrong Creek at Mouth VP67JK 1.01 x 1011 43 29 

96.5 6.9 x 1010 

Armstrong Creek below 

Hatchery 

VP67JK Note 1 23 66 100 Note 1 

1.2 6.7 x 107 Harvey Creek at Grandview HD76OJ 2.33 x 10 

10 38 76 

98.8 5.5 x 109 

Note 1: Insufficient flow data to calculate load 

D. North and South Forks of the Stillaguamish River and Jim Creek 

Water Body WBID Current 

Bacteria 

Load 

(cfu/day) 

Loading Capacity: 

Target Geometric 

Mean (cfu/100 

mL) 

Total 

Percent 

Reduction 

Required 

Percent of 

Load 

(estimate) 

Wasteload 

or Load 

Allocation 

2.1 2.5 x 1010 1.5 1.8 x 1010 

N Fork Stilly (at mouth) WO38NV 1.95 x 1012 28 38 

96.4 1.2 x 1012 

5.6 1.2 x 1011 2.9 6.0 x 1010 

S Fork Stilly (at mouth) SN06ZT 2.24 x 1012 40 7 

91.5 1.9 x 1012 

1.6 5.5 x 109 Jim Creek at mouth JU33JU 4.0 x 10 

11 34 14 

98.4 3.4 x 1011 
Page xx Stillaguamish Bacteria and DO TM

Table ES-4. Load Allocations for Stillaguamish Reaches with pH Impairments 

Water Body WBID 

Loading Capacity (Total Phosphorus) 

Target Value 

Total Phosphorus 

(median seasonal 

value) 

Percent of 

Load 

(estimate) 

Load Allocation 

(Total Phosphorus

North Fork Stillaguamish 70 14 lb/day 

River (km 15.2-28.3) 

WO38NV 20 lb/day 0.01 mg/L 

30 6 lb/day 

Table ES-5. Load Allocations for Stillaguamish Reaches with Mercury Impairments 

Water Body WBID Loading Capacity Target Value 

Total Suspended 

Solids 

(4-day average) 

Percent of 

Load 

(estimate) Load Allocation 

Stillaguamish River QE93BW 65 mg/L 

North Fork Stillaguamish 

(upper – above RM 20) 

WO38NV 13 mg/L 

North Fork Stillaguamish 

(lower – below Hazel slide 

at RM 20) 

WO38NV 65 mg/L 

South Fork Stillaguamish 

(mouth) 

SN06ZT 65 mg/L 
Stillaguamish Fecal and DO TMDL Submittal Report Page 1

Introduction 

The Stillaguamish River basin includes portions of Snohomish and Skagit counties in 

Washington State (Figure 1). Several rivers and streams in the Stillaguamish River basin were 

on Washington State’s 1996 and 1998 Section 303(d) list because of violations of one or more 

water quality criteria (Table 1). 

In 2000, the Washington State Department of Ecology (Ecology) Water Quality Program 

selected the basin for a total maximum daily load (TMDL) assessment. Ecology’s 

Environmental Assessment Program was asked to design and conduct the TMDL evaluation. 

Two TMDL projects emerged, based on personnel resources and analytical approaches for the 

303(d)-listed parameters: (1) a temperature TMDL (Pelletier and Bilhimer, 2004), and 

(2) this TMDL evaluation of fecal coliform, dissolved oxygen, pH, arsenic, and mercury. 

The TMDL analysis of listings for ammonia, lead, copper, and nickel in the Old Stillaguamish 

River (Table 1) was originally planned to be included in this evaluation (Joy, 2001). However, 

these analyses were postponed because of new infrastructure on the channel. (In 2003 the local 

Flood Congrol District installed a tide gate mecha ism in the channel to increase freshwater flow 

during the low-flow season. And in 2004 the city of Stanwood completed an upgrade of its 

wastewater treatment plant.) The Old Stilly Chanel TMDL field work and water qhality 

sampling will be initiated in summer 2006. New water quality data are required to better reflect 

current conditions in the channel, and to set load and wasteload allocations more accurately. 

Mercury was added to the list of possible pollutants in the basin, even though mercury was not 

on the 303(d) list. Local concern was generated by data presented in a report by the Puget Sound 

Water Quality Action Team (1998). Those data were collected by Ecology but also qualified as 

estimated values by Ecology (Joy, 2001). More recent mercury data were not available to make 

a proper water quality evaluation. 

Section 303(d) of the federal Clean Water Act mandates that the state establish TMDLs for 

surface waters that do not meet standards after application of technology-based pollution 

controls. The U.S. Environmental Protection Agency (EPA) has promulgated regulations 

(40 CFR 130) and developed guidance (EPA, 1991) for establishing TMDLs. 

Under the Clean Water Act, every state has its own water quality standards designed to protect, 

restore, and preserve water quality. Water quality standards consist of designated uses, such as 

cold water biota and drinking water supply, and criteria, usually numeric criteria, to achieve 

those uses. When a lake, river, or stream fails to meet water quality standards after application 

of required technology-based controls, the Clean Water Act requires the state to place the water 

body on a list of "impaired" water bodies and to prepare an analysis called a TMDL. 

The goal of a TMDL is to ensure the impaired water will attain water quality standards. A 

TMDL includes a written, quantitative assessment of water quality problems and of the pollutant 

sources that cause the problem. The TMDL determines the amount of a given pollutant that can 

be discharged to the water body and still meet standards (the loading capacity) and allocates that 
Page 2 Stillaguamish Fecal and DO TMDL Submittal Report 

load among the various sources. If the pollutant comes from a discrete source (referred to as a 

point source) such as a municipal or industrial facility’s discharge pipe, that facility’s share of 

the loading capacity is called a wasteload allocation. If it comes from a set of diffuse sources 

(referred to as a nonpoint sources) such as general urban, residential, or farm runoff, the 

cumulative share is called a load allocation. 

Table 1. Stillaguamish River basin (Water Resource Inventory Area 5) and Port Susan (WRIA 6) 

water bodies on the 1998 Section 303(d) list for TMDL evaluations. Listing status in 1996 is also 

indicated for individual parameters. 

Old ID No. New ID No. Name Parameters 1996 

303(d) 

WA-05-1021 PA13UD Deer Creek Temperature Yes 

WA-05-1016 QJ28UC Fish Creek Fecal Coliform Yes 

 HD76OJ Harvey Creek Fecal Coliform No 

WA-05-1025 BH79GG Higgins Creek Temperature Yes 

 JU33JU Jim Creek Fecal Coliform No 

WA-05-1012 GH05SX Jorgenson Slough 

(Church Creek) 

Fecal Coliform Yes 

WA-05-1023 EX67XM Little Deer Creek Temperature Yes 

 IJ55EP Lake Martha Creek Fecal Coliform No 

 QE93BW Old Stillaguamish River Fecal Coliform, Ammonia, 

Lead, Copper, Nickel 

No 

WA-05-1018 VJ74AO Pilchuck Creek Temperature, Dissolved Oxygen No 

WA-PS-0020 390KRD Port Susan Fecal Coliform Yes 

WA-05-1015 OT80TY* Portage Creek Fecal Coliform, 

Dissolved Oxygen, Turbidity

Yes 

WA-05-1010 QE93BW Stillaguamish River Fecal Coliform, Temperature, 

Dissolved Oxygen, Arsenic

Yes/Yes 

Yes/No 

WA-05-1010 ZO73WL Stillaguamish River 

(Hat Slough) 

Fecal Coliform, Temperature, 

Dissolved Oxygen

No/No 

Yes 

WA-05-1020 WO38NV N.F. Stillaguamish River Fecal Coliform Yes 

WA-05-1020 XN66YN N.F. Stillaguamish River Temperature Yes 

WA-05-1050 SN06ZT S.F. Stillaguamish River Fecal Coliform, Temperature, 

pH, Dissolved Oxygen

Yes/Yes 

Yes/No 

WA-05-9160 350KXA Sunday Lake Total Phosphorus, Total Nitrogen No 

 LU17DC Unnamed Creek #0456 Fecal Coliform No 

* Includes the listings mistakenly assigned to OJ28UC, Fish Creek, and YF03BC, a branch of Portage Creek, 

but should have been entered as OT80TY, Portage Creek. 

Bold - parameters are 303(d) listings addressed in this report. 

The TMDL must also consider seasonal variations and include a margin of safety that takes into 

account any lack of knowledge about the causes of the water quality problem or its loading 

capacity. A reserve capacity for future loads from growth pressures is sometimes included as 

well. The sum of the wasteload and load allocations, the margin of safety, and any reserve 

capacity must be equal to or less than the loading capacity. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 3

Figure1. Generalized land cover in the study area 
Page 4 Stillaguamish Fecal and DO TMDL Submittal Report 
Stillaguamish Fecal and DO TMDL Submittal Report Page 5

Background 

Setting 

The Stillaguamish River watershed covers 1770 km2

 and extends from sea level to 2,086 meters 

in elevation on Whitehorse Mountain in the Squire Creek drainage. It is the fifth largest tributary 

to Puget Sound. The Stillaguamish River has two major forks at river kilometer 28.6 (river mile 

17.8); the North Fork drains 736 km2, and the South Fork drains 660 km2. Average annual 

precipitation in the watershed ranges from about 80 cm/year (about 30 inches/year) at lower 

elevations to about 380 cm/year (150 inches/year) at higher elevations (Figure 2) (Pess et al., 

1999). 

Headwater streams are typically steep (>0.2 m/m) and relatively small (bankfull width < 5 m, 

Pess et al., 1999). Channel slopes decrease dramatically (between 0.01 and 0.06 m/m) as streams 

traverse terraces carved into valley-filling glacial and alluvial deposits (Figure 3), and channels 

become larger as tributaries coalesce. 

The geology of the Stillaguamish basin has been briefly described in the Salmon Habitat 

Limiting Factors Analysis (Washington Conservation Commission, 1999): 

“The North Cascades include high grade Mid-Cretaceous to Paleocene melange rocks that 

dominate west of the Darrington Fault. East of the fault the dominant rock unit is the 

Darrington Phyllite, a metamorphic rock type that dominates the upper North Fork 

Stillaguamish. This rock is particularly prone to erosion, which is a major problem in this 

watershed. Crystalline rocks of the Oligocene Squire Creek stock form the south side of the 

North Fork and the north side of the upper South Fork Stillaguamish. 

Glacial outwash from the Puget Lobe of the Cordilleran ice sheet forms the terraces in the forks 

and the topography of the lower watershed. Younger alluvial deposits are inset within the 

terraces in the wider portions of the valleys of the forks. The mainstem of the Stillaguamish 

flows through an alluvium-floored valley 1.5-3 km wide, inset within terraces of glacial outwash. 

The clay, silt and sand deposits of glacial and lake origin are the main source of the significant 

sediment production in the watershed (Perkins and Collins 1997). In the steeper sloped areas, 

these deposits are particularly prone to landslides, which are a significant problem for fisheries 

in this drainage. “ 

Soils types vary widely but follow the patterns of the underlying geology. The valley soils over 

alluvial deposits tend to have low permeability; i.e., Hydrologic Group C and D soils 

predominate along the valley floors of the North Fork, lower South Fork, and along the 

mainstem and lower mainstem tributaries to Port Susan. More permeable Hydrologic Group A 

or B soils are found on the plateaus and hillsides. 

The mountainous upper watershed contributing to the forks are primarily public forest lands 

(Figure 4). The U.S. Forest Service manages 697 km2

 (269 mi2) within the Mount BakerSnoqualmie National Forest, and the Washington State Department of Natural Resources (DNR) 

manages 210 km2 (81 mi2). Timber harvesting and recreational uses predominate. Only inactive 
Page 6 Stillaguamish Fecal and DO TMDL Submittal Report 

and abandoned mines remain in once active metal mining areas near the headwaters of both forks 

(McKay, Jr., Norman, Shawver, and Teissere, 2001). Lower elevation forests (< 700m) are 

within the western hemlock zone (Franklin and Dyrness, 1973). Dominant conifer species in 

these forests are western hemlock, Douglas-fir, western red cedar, and Sitka spruce. Deciduous 

trees include red alder, black cottonwood, and bigleaf maple. Middle elevation forests 

(700-1300m) are in the silver fir zone, and higher elevations (> 1300m) are in the alpine fir zone. 

Granite Falls (population est. 2,915) and Darrington (population est. 1,385) have growth 

management areas that influence some residential development in the upper basin along the 

valley floors (Figure 1). Other small residential, business, and agricultural properties are 

scattered the length of the valleys. The U.S. Department of Defense controls approximately 

18.1 km2 (7 mi2) in the Jim Creek sub-basin of the South Fork. The Indian Ridge Corrections 

Center with its wastewater facility is also located in the Jim Creek sub-basin. 

The South Fork enters a floodplain 6.4 km (4 miles) before the confluence with the North Fork. 

The mainstem at the confluence is at an elevation of 15.4 m (51 ft), and the gradient is fairly 

even to the mouth at Port Susan. Dikes are common along the length of the mainstem. The 

floodplain has visible evidence of historical meanders and sloughs. 

Port Susan is bounded on the north and west by Camano Island. It is a shallow, poorly flushed 

bay that extends from South Pass at Stanwood to Port Gardner at Everett. Low-density 

residential and agriculture are the most common land uses around the bay. No commercial 

shellfish harvesting operations are currently permitted in Port Susan, but recreational harvesting 

occurs. 

The primary riparian land use along the mainstem and lower reaches of the major forks is 

agriculture. The lower basin has diverse land uses, and most land is privately owned. Arlington 

(population est. 14,330) and Stanwood (population est. 4,190) have active urban growth areas. 

In 1995, Stienbarger (1995) estimated there were at least 909 commercial and non- commercial 

farms in the lower basin. Agriculture is still quite active in the lower basin, but conversions from 

agriculture to rural residential or non-commercial farm uses are becoming common along the 

Interstate 5 corridor. The DNR controls approximately 72.5 km2

 (28 mi2) in the Pilchuck Creek 

sub-basin. Privately held forests are scattered throughout the upper reaches of other tributaries 

as well. 

The Stillaguamish Tribe, Sauk-Suiattle Tribe, and Tulalip Tribes have cultural and economic 

interests in the Stillaguamish River basin. The Stillaguamish Tribe offices are located in 

Arlington, the Sauk-Suiattle Tribe offices in Darrington, and the Tulalip Tribes offices on the 

Tulalip Indian Reservation immediately south of the basin. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 7

Squire Creek

Jim Creek

Canyon Creek

Stillaguamish River

Pilchuck Creek

North Fork Stillaguamish River

South Fork Stillaguamish River

Deer Creek

5 0 5 10 Kilometers

average annual precipitation (cm/year)

80 - 120 cm/year

120 - 160

160 - 200

200 - 240

240 - 280

280 - 320

320 - 360

360 - 400

Figure 2. Annual average precipitation in the Stillaguamish River watershed (data from 

www.daymet.org). 
Page 8 Stillaguamish Fecal and DO TMDL Submittal Report 

5 0 5 10 Kilometers

Hydrogeologic units

Alluvial deposits

Alpine glacial deposits

Bedrock deposits

Bog, marsh, and peat deposits

Lahar deposits

Pre-Fraser undifferentiated non-glacial deposits (predominately fine grained)

Vashon advance outwash deposits (predominately coarse grained)

Vashon recessional outwash deposits (predominately coarse grained)

Vashon recessional outwash deposits (predominately fine grained)

Vashon till deposits (predominately fine grained)

Water bodies

major streams

Figure 3. Surface hydrogeology of the Stillaguamish River watershed. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 9

5 0 5 10 Kilometers

land ownership

private

federal

state

tribe

major streams

Figure 4. Land ownership in the Stillaguamish River watershed. 

At kilometer 4.4 (river mile 2.75) is another important hydrologic feature, a split between the 

Old Stillaguamish Channel and Hat Slough. Most flow was redirected out of the Old 

Stillaguamish Channel by a series of major floods that released logjams more than 70 years ago. 

Hat Slough provided a straight path to Port Susan for the floodwaters and now is the primary 

channel of the river. The Old Channel meanders for 12.9 km until it bifurcates at about river 

kilometer 2.4; South Pass transports about 80% of the flow to and from Port Susan; and West 

Pass carries the remaining flow to and from Skagit Bay. 

During the dry season, the Old Channel is almost a tidal slough; namely, Church Creek, Miller 

Creek, and intermittent Stanwood Wastewater Treatment Plant (WWTP) effluent discharges are 

the only additional freshwater inflows to a small amount of Stillaguamish River inflow. During 

the wet season, water from the Stillaguamish River floods into this remnant channel and flushes 

it. With fewer flood events in the past couple of years, the remnant channel has experienced a 

build up of sediment and vegetation. As mentioned in the Introduction, the flood control district 

installed a tide gate to help entrain more freshwater in the Old Channel from the Stillaguamish 

River. Measurements of dissolved oxygen in summers of 2003 and 2004 by the 
Page 10 Stillaguamish Fecal and DO TMDL Submittal Report 
Stillaguamish Fecal and DO TMDL Submittal Report Page 11

Stillaguamish Tribe suggests that the new tide gate may be associated with water quality 

improvement. 

Both Hat Slough and the Old Stillaguamish Channel via South Pass transport Stillaguamish 

River water to Port Susan. The Warm Beach area south of Hat Slough and Camano Island to the 

west also contribute run-off through several small drainages to Port Susan, and they are 

considered part of the Stillaguamish water quality management area. Port Susan is a relatively 

shallow and poorly flushed bay. For several years, commercial shellfish harvesting has been 

restricted or prohibited in the bay by the Washington State Department of Health because of 

fecal coliform contamination in the water column. Port Susan currently is not classified since 

shellfish are no longer commercially harvested. 

Flows 

Ecology installed a network of flow gauging stations during 2001 as described in Pelletier and 

Bilhimer (2001) (Figure 5). The gauges were placed in coordination with U.S. Geological 

Survey (USGS) and Snohomish County gauge sites. 

The USGS currently gauges flows in the North Fork Stillaguamish River near Arlington (station 

12167000) and in the South Fork Stillaguamish River near Granite Falls (station 12161000 - 

gage heights only). Some Ecology gage sites were placed at historical USGS sites to verify flow 

network relationships. Snohomish County also measures gauge heights at several sites, but the 

discharge volume records for these sites have not been determined. 

The USGS has historically gauged flows at several other stations in the watershed on an 

intermittent basis (Figure 5). Only one historical gauging station, the Stillaguamish River near 

Silvana, was established in the mainstem Stillaguamish River below the confluence of the forks. 

Continuous discharge data for the station (USGS #12167700) were only recorded over 

15 months, but USGS and Ecology have kept rating curves current for instantaneous flow 

measurements. There are statistically strong correlations between flows at the long-term gages 

in the upper basin and the intermittent data collected at the Silvana gage site (Figure 6). 
Page 12 Stillaguamish Fecal and DO TMDL Submittal Report 

U%

UU

%%

U%

U%

U%

U%

U% S#

S#

S#

S#

S#

12161000

12162500

12164000

12165000

12166500

12167000

12167700

12168500

Squire Creek

Jim Creek

Canyon Creek

Stillaguamish River

Pilchuck Creek

North Fork Stillaguamish River

South Fork Stillaguamish River

Deer Creek

05D01

05P01

05NF07

05SF02

05SF05

5 0 5 10 Kilometers

U% USGS flow gage

S# Ecology flow gage

Figure 5. Flow gauging stations in the Stillaguamish River watershed. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 13

100

1000

10000

100000

Mar-00

May-00

Jul-00

Sep-00

Nov-00

Jan-01

Mar-01

May-01

Jul-01

Sep-01

Nov-01

Date

Discharge (cfs)

North Fork

Silvana (est.)

I-5 Instantaneous

Figure 6. A daily mean discharge hydrograph for the Stillaguamish River 

near Silvana created from the discharge record at the North Fork Stillaguamish River near 

Arlington (USGS #12167000), compared to instantaneous measurements calculated from the 

wire-weight gage readings at Silvana in 2000 and 2001. 

Flows in the Stillaguamish River respond to rainfall and snowmelt. There are no large storage or 

diversion structures in the basin. Small glaciers and snowfields at the highest elevations, and 

ground water in the lower valleys supply water during the lowest flow periods. Approximately 

75% of the annual precipitation falls between October and March (Washington Conservation 

Commission, 1999). Mean daily flows recorded for the two long-term USGS gauge stations on 

the North and South forks show a similar monthly pattern (Table 2). Peak flows occur during 

short-term storms or rain-on-snow events. The lowest flows occur during late summer to early 

fall (August through October), before the fall rainstorms arrive. The annual seven-day, ten-year, 

low-flow statistics were estimated at USGS stations with greater than ten years of flow data 

(Table 3). 

Table 2. Mean daily discharge (in cfs) by month for two long-term USGS gauge stations on the North 

Fork and South Fork Stillaguamish River. 

Station Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec 

North Fork 

Stillaguamish 

12167000 

2,777 2,447 2,131 2,203 2,176 1,661 876 463 677 1,512 2,756 3,055 

South Fork 

Stillaguamish 

12161000 

1,419 1,208 1,069 1,201 1,361 1,140 599 299 484 985 1,421 1,663 
Page 14 Stillaguamish Fecal and DO TMDL Submittal Report 
Stillaguamish Fecal and DO TMDL Submittal Report Page 15

Table 3. Summary of the annual 7-day, 10-year (7Q10), low-flow statistics for USGS gauging stations in 

the Stillaguamish River basin. 

Station Station Name Period Drainage 

area (km2) 

7Q10 low (1)

 cms (cfs) 

12161000 South Fork Stillaguamish River near Granite Falls 1928 – 1980 308 2.237 (79) 

12162500 South Fork Stillaguamish River above Jim Creek 1936 – 1957 515 3.427 (121) 

12164000 Jim Creek near Arlington 1937 – 1957 120 0.193 (6.8) 

12167000 North Fork Stillaguamish River near Arlington 1928 – 2001 679 4.956 (175) 

(1) Calculated using Log Pearson III frequency factor or distribution-free methods (Aroner, 2002) 

Tributaries in the lower valley respond to storm events and ground water inflow. Residential 

development in some sub-basins may be creating ‘flashier’ hydrographic responses to storm 

events, and less extended seasonal storage from ground water. 

Water Withdrawals 

Actual water withdrawals at any given time from streams in the Stillaguamish River watershed 

are not known, but information from the Water Rights Application Tracking database system 

(WRAT) was used as an indicator of the amounts of water that may be withdrawn. The water 

quantity potentially withdrawn from surface waters for consumptive use is about 2.2 cms from 

surface waters and 1.6 cms from ground water (Table 4). Irrigation represents the majority of the 

consumptive withdrawal from surface waters. 
Page 16 Stillaguamish Fecal and DO TMDL Submittal Report 

Table 4. Summary of consumptive water rights in the Stillaguamish River watershed 

(Pelletier and Bilhimer, 2004).

Total of all 

Tributaries water right flows 

(cfs) (cms) 

Consumptive surface water 

withdrawals 

Alder Brook 4.06 0.115 

Armstrong Creek 0.84 0.024 

Bulson Creek 0.02 0.001 

Canyon Creek 0.12 0.003 

Edwards Creek 3.93 0.111 

Fish Creek 3.68 0.104 

French Creek 0.02 0.001 

Hat Slough 15.52 0.439 

Jim Creek 0.64 0.018 

Lake Cavanaugh 0.05 0.001 

Lake Creek 0.39 0.011 

Lake Martha 0.01 0.0003 

March Creek 1.23 0.035 

Miller Creek 0.01 0.0003 

NF Stillaguamish River 26.43 0.748 

Pilchuck Creek 0.54 0.015 

Port Susan 1.10 0.031 

Portage Creek 1.33 0.038 

SF Stillaguamish River 7.64 0.216 

South Pass 1.00 0.028 

South Slough 5.80 0.164 

Stillaguamish River 0.30 0.009 

Other 6.62 0.187 

Total 81.27 2.300 

 

Total consumptive 

groundwater withdrawals 56.40 1.600 

Potential Pollutant Sources 

There are several potential point and nonpoint sources in the basin that could contribute to the 

Stillaguamish basin Section 303(d) listings. Wastewater treatment plants (WWTPs) and dairies 

historically have been the focus of water quality actions in the lower basin and along the upper 

basin valleys to control bacteria, nutrients, and oxygen demand inputs. However, properties near 

Arlington and Stanwood are rapidly converting from agricultural to rural residential uses. 

Wastewater management practices and stormwater runoff issues in these areas of the basin have 

not necessarily meant a reduction of pollutant loads as much as a change in the delivery 

mechanisms and dispersal of pollutants sources. 

Point sources include WWTPs with distinct collection and discharge points where pollutants 

under permit can be monitored. Point sources in the Stillaguamish basin include the WWTPs at 
Stillaguamish Fecal and DO TMDL Submittal Report Page 17

Arlington, Indian Ridge Correctional Facility, Warm Beach Christian Conference Center, 

Twin City Foods, and Stanwood. All have current National Pollutant Discharge Elimination 

System (NPDES) or State Waste Discharge permits. The operational units and permit limits for 

these facilities are described in Appendix A. All facilities are self-monitored and report to 

Ecology under current permit requirements. Most permits require effluent monitoring of pH, 

temperature, biochemical oxygen demand (BOD), total suspended solids, fecal coliform bacteria, 

and disinfection residuals. None of the facilities currently have permit limits on nutrient 

concentrations. 

Stillaguamish River basin point sources other than WWTPs that discharge to surface water under 

current NPDES permits are listed in Appendix F. 

The WWTPs have been improving over the years to reduce bacteria, biochemical oxygen 

demand, and ammonia inputs into receiving waters. Increased housing densities and expanding 

utilities within the municipal service areas also have required the municipal WWTPs to increase 

their treatment capacities. Arlington WWTP completed an upgrade of its facility in 1998, and 

Stanwood completed an upgrade in 2004. The Warm Beach Conference Center upgraded its 

lagoon system by adding a wetland treatment unit in 2003. The Indian Ridge facility underwent 

a change in operational management in 2000. Twin City Foods in Stanwood has used an 

upgraded treatment lagoon and land application system for food processing waste, non-contact 

cooling water, and repack water since 1998. 

Certain classes of stormwater systems are now considered point sources, although the 

contaminants are often released in an uncontrolled and dispersed manner. Snohomish County 

and the Washington State Department of Transportation (WSDOT) were required to implement a 

stormwater management program under Phase 1 of the NPDES and State Waste General 

Stormwater Permit process in 1995. Snohomish County has monitored and implemented 

improvements in several areas of the Stillaguamish basin with stormwater drainage and nonpoint 

runoff problems (Snohomish County, 2002). WSDOT and Snohomish County Public Works 

Department recognize that stormwater runoff from roads and adjacent properties have 

increasingly become a problem, especially along the Interstate 5 corridor. WSDOT has 

inventoried many highway stormwater drains located in Pilchuck Creek, Portage Creek, Church 

Creek, Harvey/Armstrong Creek, and North Fork Stillaguamish River sub-basins. 

Stormwater quality and quantity from roadway runoff and uncontrolled runoff from land 

adjacent to ditches and drains have probably always been a problem for the county and 

municipal collection systems. More recently, it has been identified as a problem in areas of the 

county where new residential development has occurred and where non-commercial farms are 

located. Storm water can be significant sources of fecal coliform bacteria, nutrients, metals, 

suspended solids, and oxygen demanding particles. Large and sudden quantities of stormwater 

runoff can disrupt natural hydrologic cycles and can ruin stream channel aquatic biota habitat. 

Snohomish County and the Snohomish Conservation District have been working together to 

mitigate stormwater contaminant loads. For example, Glade Bekken, a small sub-basin near the 

mouth of the Stillaguamish River, was host to a number of watershed restoration projects in 1998 

designed, in part, to repair stream habitat degraded by stormwater runoff and to reduce 

stormwater loads of fecal coliform, nitrate, and suspended solids (Thornburgh, 2001). 
Page 18 Stillaguamish Fecal and DO TMDL Submittal Report 

Arlington and Granite Falls are required under Phase 2 of the Municipal General Stormwater 

Permit process to complete plans and implement programs. Storm water from the Arlington 

municipal area historically has been routed through several storm drains to the South Fork and 

mainstem Stillaguamish River, and to drainages in the Portage and March Creek sub-basins. 

Granite Falls is located mostly in the Pilchuck River sub-basin, but some stormwater may flow 

towards the South Fork Stillaguamish River. 

Both quantity and quality effect of storm water are issues for receiving water quality. Changes 

in land use may have affected seasonal flows in Portage Creek that have resulted in more serious 

and frequent flooding (Barlond, 2001). This is common in developing areas where impervious 

structures like homes and roads increase the amount of runoff to drains and streams. Arlington 

has made some improvements in its collection system and routing, and has worked with WSDOT 

in using wetlands for stormwater treatment and flood control in some areas (Blake, personal 

communication, 2002). 

Nonpoint sources do not have easily identified and distinct locations where pollutants are 

discharged and can be monitored. Nonpoint sources are usually associated with land uses such 

as timber harvesting, construction, agricultural production, intensive recreational activities, and 

urban runoff. Many types of nonpoint sources are intermittent because they are generated by 

rainfall in sufficient amounts to produce runoff. 

A significant source of nonpoint pollution in western Washington has historically been attributed 

to dairies and animal production facilities. A steady improvement in waste management and 

operational practices at these types of facilities over the past 25 years has reduced their pollutant 

loading in many basins. The Dairy Nutrient Management Act of 1998 required all dairies in the 

state to register and have certified nutrient management plans by December 31, 2003. 

Implementing and maintaining the management plans should reduce or eliminate pollutant 

loading from dairy operations. 

The current inventory shows 21 active dairies in the Stillaguamish basin with approximately 

5100 cows and 2000 heifers and calves (Ecology, 2003a). Most of the dairies are located in the 

lower valley floodplain, but a few are located along the valley of the North Fork and clustered 

near Arlington in drainages to the South Fork. As of December 2004, all dairies had certified 

nutrient management plans. Only one dairy in the basin has a NPDES and state waste discharge 

general permit (WAG 01-3025B). It is located south of the Twin City Foods land application 

site between the Old Stillaguamish Channel and Hat Slough. 

There are fewer dairies in the basin now than in 1996. The 1996 dairy inventory listed 44 dairies 

with almost 8000 cows in the basin. By 1999 the number of active dairies in the basin was 

reduced to 31, with approximately 8000 cows and 3000 heifers and calves (Ecology, 2000). 

Now there are 21 active dairies. Two of the ten dairies that went out of business between 1999 

and 2000 were in the South Fork sub-basin, and one was in the Pilchuck Creek sub-basin. The 

remaining eight were in the Portage Creek sub-basin and lower Stillaguamish floodplain between 

Arlington and Stanwood. 

Between 1990 and 2000, Snohomish County’s population increased by 30% (Washington State 

Office of Financial Management, 2003). Land use in the Stillaguamish River basin has changed 

as a result of that population growth. Properties are being converted from commercial 
Stillaguamish Fecal and DO TMDL Submittal Report Page 19

agricultural and forestry uses to high and low density residential, non-commercial agriculture, 

and commercial/industrial uses. 

These land use conversions may not necessarily result in reduced loading of contaminants 

traditionally associated with commercial agriculture, e.g., bacteria, nutrients, suspended solids, 

and pesticides. Rural residential areas, non-commercial agricultural interests, and 

commercial/industrial uses can generate greater loads of these same pollutants. Increased 

contaminant loading can be related to poor animal-keeping practices on smaller lots – anything 

from a pet horse or family cow to a boarding stable. These sources, along with poorly 

maintained and failing on-site septic systems, can be directly discharged into waterways. 

Background concentrations of some contaminants in the basin complicate some aspects of the 

TMDL. Although inactive and abandoned mines could be potential sources of uncontrolled 

contamination, veins of arsenic and mercury-enriched bedrock in the headwater streams and 

aquifers of both forks may be responsible for some elevated concentrations of these metals. 

Riparian wetlands and groundwater seepage into small tributaries could be natural sources of 

lower dissolved oxygen concentrations during baseflow conditions. The diked flats used by 

Twin City Foods and the other farmlands in the lower Stillaguamish Valley provide an excellent 

wintering area for flocks of trumpeter swans, snow geese, and other waterfowl. The riparian 

areas, wetlands, sloughs, and tideflats of Port Susan provide an excellent habitat for seals and 

other wildlife, also a potential for significant seasonal bacteria loading. 

Relatively narrow veins of metal ore in the Cascade Mountains, where headwater streams of the 

basin originate, are also rich with arsenic and mercury. Where tributaries and snowmelt cross 

these veins, contamination is possible. One potential anthropogenic source for arsenic and 

mercury contamination may be historical mining operations in the mountains along the veins. 

Huntting (1956) shows several historical mines in the South Fork and North Fork Stillaguamish 

River basins where arsenic and mercury were of secondary value. Metal mining was most active 

in the late 1800s until the 1920s. No active mines are located in the headwaters. The 

Washington State Department of Natural Resources, Ecology, the EPA, and other federal 

agencies are making an inventory and monitoring water quality in these inactive and abandoned 

mining areas (Norman, 2000; Raforth, Norman, and Johnson, 2002). 

Another potential source of arsenic and mercury is ground water. Elevated groundwater arsenic 

concentrations have been a well-known problem in the Granite Falls area where completed wells 

are in contact with the bedrock formations or bedrock-derived material (Snohomish County 

Health District and Washington State Department of Health, 1991). The elevated arsenic 

concentrations in ground water are more widespread in Snohomish County than the Granite Falls 

area (Thomas, Wilkinson, and Embrey, 1997). Some wells in the Cascade foothills between 

Arlington and Granite Falls had elevated arsenic. Elevated mercury was detected in two of the 

wells north of Stanwood and another well in the North Fork valley. The sources of arsenic and 

mercury in these samples were not determined; sampling protocols and quality assurance were 

followed and acceptable. 

Wildlife can contribute a significant load of bacteria, nutrients, and oxygen-demanding 

substances when they are found in large numbers. The first small flocks of snow geese arrive on 

the Skagit-Fraser estuaries in late September and build in numbers throughout October and early 
Page 20 Stillaguamish Fecal and DO TMDL Submittal Report 

November. A small portion move on, and then the population is relatively stable until spring. 

This flock numbered about 41,100 during 1987-96 (WDFW, 2003). With other flocks of geese, 

swans, and ducks joining the snow geese, the populations of waterfowl wintering in the lower 

Stillaguamish waterways and adjacent fields are substantial. In Table 5, three to five years of 

Audubon bird counts and special inventories by the Washington Department of Fish and Wildlife 

in northeast Port Susan, Livingston Bay, and the lower Stillaguamish Delta were compiled and 

summarized by the Audubon Society (Cullinan, 2001). 

Table 5. Bird population data for northeast Port Susan, Livingston Bay, and the Stillaguamish River delta 

(Cullinan, 2001). 

Bird Season Sighted Average 

Number 

Maximum 

Number 

Trumpeter 

Swan 

Winter 51 139 

Snow Goose Winter 9,700 25,000 

Ducks Winter 4,040 6,864 

Eagle Winter 4 10 

Merlin Winter 1 3 

Falcon Winter 1 2 

Shorebirds Fall Migration - 50,000 

Shorebirds Winter 24,175 31,050 

Shorebirds Spring Migration 34,350 50,000 

About 300 harbor seals are residents of northern Port Susan. Their population has stabilized 

since 1993 or 1994 (Huber, personal communication, 2003). They haul-out on the tideflats in 

warmer months, pup in July and August, and stay around northern Port Susan throughout the 

year. In cooler months they spend most of their time in the water. Less is known about their 

dispersal within Port Susan during the winter months since they are in the water during the day, 

and lower tides (when they might move out of the water) occur at night. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 21

Applicable Water Quality Criteria 

The Water Quality Standards for Surface Waters of Washington State are published pursuant to 

Chapter 90.48 of the Revised Code of Washington (RCW) (Ecology, 1997). Ecology has the 

authority to adopt rules, regulations, and standards as necessary to protect the environment. 

Under the federal Clean Water Act, the EPA regional administrator must approve the water 

quality standards adopted by the state (Section 303 (c) (3)). State water quality standards 

designate certain characteristic uses for protection and specify the criteria necessary to protect 

those uses (Washington Administrative Code (WAC), Chapter 173-201A). 

This report addresses impairments of characteristic uses caused by fecal coliform bacteria, 

dissolved oxygen, pH, arsenic, and mercury as pollutants. The characteristic uses designated by 

Washington State for protection in Stillaguamish River basin streams (Class AA and Class A) 

and for Port Susan (Class A marine waters) are as follows (Chapter 173-201A WAC): 

"Characteristic uses. Characteristic uses shall include, but not be limited to, the following: 

(i) Water supply (domestic, industrial, agricultural). 

(ii) Stock watering. 

(iii) Fish and shellfish: 

 Salmonid migration, rearing, spawning, and harvesting. 

 Other fish migration, rearing, spawning, and harvesting. 

 Clam and mussel rearing, spawning, and harvesting. 

 Crayfish rearing, spawning, and harvesting. 

(iv) Wildlife habitat. 

(v) Recreation (primary contact recreation, sport fishing, boating, and aesthetic 

 enjoyment). 

(vi) Commerce and navigation." 

Washington State has water quality criteria (Chapter 173-201A WAC) for fecal coliform 

bacteria, dissolved oxygen, pH, and metals to protect these characteristic uses (Table 6). 

Human-health criteria for arsenic and mercury are set by the EPA through the National Toxics 

Rule (40 CFR 131.36). The most recent version of Washington’s water quality standards was 

adopted in November 1997. Ecology submitted updated water quality standards to EPA for 

approval in July 2003. The new criteria cannot be implemented until they are approved by EPA. 

In a January 12, 2005 letter, EPA approved only a partial set of the recently adopted water 

quality standards; Table 6 reflects the current standards including the January 2005 approved 

standards. 

Other sections of Chapter 173-201A WAC are pertinent to the parameters in the Stillaguamish 

TMDL. Chapter 173-201A-070, a section on antidegradation, states that existing beneficial uses 

shall be maintained and protected, and no further degradation is allowed, and also states that 
Page 22 Stillaguamish Fecal and DO TMDL Submittal Report 

"Whenever the natural conditions of said waters are of a lower quality than the criteria 

assigned, the natural conditions shall constitute the water quality criteria." 

Table 6. Current state water quality (Chapter 173-201A WAC) and National Toxics Rule 

(40 CFR 131.36) criteria used to determine if Stillaguamish River basin waters and Port Susan are 

supporting beneficial uses. Marine criteria apply to Port Susan. 

Criteria Category Statistic Criterion Ancillary Data Required 

Dissolved oxygen 

Class B Freshwater Minimum 6.5 mg/L 

Class A Freshwater Minimum 8.0 mg/L 

Class AA Freshwater Minimum 9.5 mg/L 

Class A Marine Minimum 6.0 mg/L 95% vertically avg. daily max. salinity > 1ppt 

Fecal coliform 

Class A (Primary Contact 

Recreation) Freshwater Geometric mean 100 cfu/100 mL 

Not more than 10% of 

the samples exceed* 200 cfu/100 mL 

Class AA Freshwater Geometric mean 50 cfu/100 mL 

Not more than 10% of 

the samples exceed* 100 cfu/100 mL 

Class A Marine Geometric mean 14 cfu/100 mL Vertically averaged salinity ≥ 10 ppt 

Not more than 10% of 

the samples exceed* 43 cfu/100 mL 

FDA Shellfish harvesting Geometric mean 14 MPN/100 mL 

 90th percentile value 43 MPN/100 mL 

pH 

Freshwater Maximum 8.5 

 Minimum 6.5 

Marine Maximum 7.0 

 Minimum 8.5 

Arsenic 

Freshwater Aquatic Toxicity 4-day average/3 years 150 ug/L Dissolved arsenic (EPA, 1999 revision) 

 1-hr average/3years 340 ug/L Dissolved arsenic (EPA, 1999 revision) 

Marine Aquatic Toxicity 4-day average/3 years 36 ug/L 21 ug/L to prevent non-lethal effects to diatoms 

 1-hr average/3years 69 ug/L 95% vertically avg. daily max. salinity > 1ppt 

Human Health ** Maximum 0.018 ug/L Consumption of water and organisms 

Human Health ** Maximum 0.14 ug/L Consumption of organisms only 

Mercury 

Freshwater Aquatic Toxicity 4-day average/3 years 0.012 ug/L 

 1-hr average/3years 2.1 ug/L 

Marine Aquatic Toxicity 4-day average/3 years 0.025 ug/L 95% vertically avg. daily max. salinity > 1ppt 

 1-hr average/3years 1.8 ug/L 95% vertically avg. daily max. salinity > 1ppt 

Human Health ** Maximum 0.14 ug/L Consumption of water and organisms 

Human Health** Maximum 0.15 ug/L Consumption of organisms only 

* The 90th percentile is statistically similar to the criteria wording that states that not more than 10% of the samples used to 

calculate the geometric mean shall exceed the numerical criterion. 

** National Toxics Rule human-health criteria: arsenic calculated at the suggested lifetime carcinogenic risk of 1:1,000,000. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 23

This is in recognition that non-anthropogenic sources like wetland and groundwater sources can 

influence local water quality conditions so that not all numeric criteria and standards are met at 

all times. In cases where dissolved oxygen concentrations are lower than the criteria due to 

natural conditions, Ecology TMDL policy (TMDL Workgroup, 1996) and the proposed state 

water quality criteria [Chapter 173-201A-200(1)(d)(i) WAC] allow up to 0.2 mg/L loss from 

cumulative anthropogenic sources. 

Chapter 173-201A also contains a narrative criterion for each classification that states: 

"Toxic, radioactive, or deleterious material concentrations shall be below those which have the 

potential either singularly or cumulatively to adversely affect characteristic water uses, cause 

acute or chronic conditions to the most sensitive biota dependent upon those waters, or 

adversely affect public health, as determined by the department." 

The narrative criteria statements acknowledge that measures of water quality other than those 

specifically addressed as numerical criteria can be used to measure compliance with the water 

quality standards. One example is that Washington State water quality standards do not have 

numeric nutrient criteria. The nutrients, nitrogen and phosphorus, are essential for plant growth 

and aquatic community health. However, when there is an overabundance of nutrients from 

point and nonpoint sources, aquatic plant growth can become over-stimulated, a process called 

cultural eutrophication. If natural re-aeration processes cannot compensate for plant respiration 

and production in areas affected by eutrophication, then dissolved oxygen concentrations plunge 

at night and become supersaturated during the day. These diel swings can be harmful to 

macroinvertebrates and fish. 

Fecal coliform criteria in marine waters are used to protect recreational uses and shellfish 

harvesting. The marine water criteria are similar for the two uses, but they are administered by 

two different state agencies in different ways. 

• Washington State Department of Health (DOH) uses the fecal coliform criteria as one 

element of the shellfish harvest area certification process. According to DOH and 

Federal Drug Administration (FDA) regulations, fecal coliform samples can only be analyzed 

by the most probable number (MPN) method. To evaluate water quality compliance, 

DOH generates running geometric mean and 90th percentile statistics at each site from 

30 consecutive samples. These statistics must consistently meet the FDA-mandated 

14 MPN/100 mL and 43 MPN/100 mL criteria, respectively. 

• Ecology uses samples analyzed by MPN or membrane filter (MF) methods. The Class A 

marine water criteria are applied to samples with salinities greater than 10 parts per thousand. 

There is no requirement for a minimum number of samples. Seasonal stratification of 

samples is required if compliance with the criteria can only be met when lower counts 

outside the season of concern are included in the sample set. 

EPA has recommended nutrient criteria for rivers and streams to address cultural eutrophication 

(EPA, 2000). The criteria have been statistically derived for the Level III ecoregions of Puget 

Lowlands and North Cascades within aggregate Ecoregion II. The EPA recommends using the 
Page 24 Stillaguamish Fecal and DO TMDL Submittal Report 

median 25th percentile of four season 25th percentiles of data collected from all stations within 

the Level III Ecoregion. The 25th percentile was considered to be roughly comparative to the 

75th percentile of reference station data until enough reference station data are analyzed (Table 

7). 

Table 7. Recommended EPA nutrient criteria for Level III ecoregions, Puget Sound and North Cascades, 

in aggregate Ecoregion II (EPA, 2000). 

Puget Lowland North Cascades Parameter 

Min Max 25th percentile Min Max 25th percentile 

Total Kjeldahl nitrogen (mg/L) 0.05 0.83 0.08 0.05 0.19 0.05 

NO2+NO3 (mg/L) 0.01 3.7 0.26 0.01 0.22 0.03 

Total nitrogen (mg/L) calculated 0.06 4.53 0.34 0.06 0.41 0.08 

Total nitrogen (mg/L) reported 0.08 2.62 0.24 0.09 0.27 0.11 

Total phosphorus (mg/L) 0.0025 0.330 0.0195 0.0025 0.042 0.003 

Chlorophyll a (ug/L) – F 0.7 0.9 0.7 NA NA NA 

Chlorophyll a (ug/L) – T NA NA NA 0.55 0.76 0.55* 

Total nitrogen – calculated = Total Kjeldahl nitrogen + NO2 + NO3 

Chlorophyll a – F = Chlorophyll a by fluorometric method with acid correction 

Chlorophyll a – T = Chlorophyll a, b, c by trichromatic method 

* = based only on one season from samples collected from less than four rivers or streams. 

The Stillaguamish River fecal coliform and dissolved oxygen TMDL incorporates measures 

other than “daily loads” to fulfill the requirements of Section 303(d). TMDLs can be expressed 

in terms of either mass per time, toxicity, or other appropriate measure. This TMDL allocates 

other appropriate measures or “surrogate measures” as provided under EPA regulations 

[40 CFR 130.2(i)]. The Report of the Federal Advisory Committee on the Total Maximum Daily 

Load (TMDL) Program (EPA, 1998) includes the following guidance on the use of surrogate 

measures for TMDL development. 

“When the impairment is tied to a pollutant for which a numeric criterion is not possible, or 

where the impairment is identified but cannot be attributed to a single traditional “pollutant,” 

the state should try to identify another (surrogate) environmental indicator that can be used to 

develop a quantified TMDL, using numeric analytical techniques where they are available, and 

best professional judgment (BPJ) where they are not.”

The 303(d) listing in the mainstem Stillaguamish River for dissolved oxygen is based on the 

criteria in Table 6. The mechanism for the loss of dissolved oxygen in the river cannot be 

directly allocated to dissolved oxygen loads since it is caused either by biological primary 

production and respiration processes (See Technical Analysis: Dissolved Oxygen, and Loading 

Capacity: Dissolved Oxygen in this report) or by direct loading of oxygen-consuming organic 

substances, which may be in the form of biochemical oxygen demand (BOD), nitrogenous 

oxygen demand (NOD), or sediment oxygen demand (SOD). For locations in the river where 

reduced oxygen concentrations result from primary production that is nutrient driven, although 
Stillaguamish Fecal and DO TMDL Submittal Report Page 25

dissolved oxygen concentration is the criterion to be met, the allocations will be to phosphorus 

and/or nitrogen loads. Where reduced oxygen conditions result from BOD loading from point 

and nonpoint sources, allocations will be for BOD, even though dissolved oxygen is the criterion 

to be met. 

In another case, fecal coliform compliance is measured by numeric criteria based on statistical 

attributes of counts at a site, i.e., both the geometric mean and “not more than 10% of the 

samples” at a site’s fecal coliform population must meet the criteria. An allocation of fecal 

coliform count loads is awkward and does not adequately address the criteria compliance 

requirements under various hydrologic conditions at the site. For example, a high fecal coliform 

count out of compliance under low-flow conditions may have a lower load than a lower count 

within compliance under higher flow conditions. Instead of managing fecal coliform sources by 

defining an acceptable load, Ecology has used the Statistical Rollback Method (Ott, 1995) to 

manage the distribution of fecal coliform counts (See Analytical Framework: Fecal Coliform). 

The approach has proven successful in past bacteria TMDL assessments (Cusimano, 1997; Joy, 

2000; and Sargeant, 2002). 

Water Quality and Resource Impairments 

Beneficial Uses and Section 303(d) Listings 

Several beneficial uses may not be meeting their full potential because of water quality 

impairments in the Stillaguamish River basin. The most important uses identified by local 

groups are salmon spawning and rearing, recreation, and shellfish harvesting. Chinook salmon 

were listed as a threatened species under the federal Endangered Species Act in 1999. Coho 

salmon are a candidate species. Commercial shellfish harvesting in Port Susan is prohibited 

because the area has not been assessed by the Washington State Department of Health since the 

mid-1980s. 

The 1998 Section 303(d)-listed parameters for water bodies in the basin are indicators that these 

uses are impaired (Table 8); additional locations in the basin (Table 9) were found to be impaired 

during the technical study for this TMDL (Ecology July 2004). Low dissolved oxygen and low 

pH can impair fish and aquatic life communities. Arsenic concentrations above human-health 

criteria can be a threat to human consumers of water, fish, and shellfish. High fecal coliform 

bacteria counts threaten primary and secondary recreational uses of the water and prevent 

shellfish harvesting. 

Salmon use a variety of habitats in the Stillaguamish, the mainstem and major forks, large and 

small tributaries, beaver ponds, riparian wetlands and side channels, estuary sloughs, and salt 

marshes. Many of these habitats have been reduced severely from sedimentation of channels by 

natural landslides and from anthropogenic activities, e.g., diking and channelization, removal of 

riparian vegetation, and water quality degradation by land use activities (Washington 

Conservation Commission, 1999). Just under one-third (1432 km) of the total stream network is 

available habitat for anadromous fish (Washington Conservation Commission, 1999). 

Salmon are present throughout the year in many parts of the basin. Table 10 shows the 
Page 26 Stillaguamish Fecal and DO TMDL Submittal Report 

approximate timing of various life-stages of salmon species in the Stillaguamish (Washington 

Conservation Commission, 1999). Rearing of several species occurs throughout the year and in 

several types of habitats. Although the spawning period overlaps between species, salmon have 

specific spawning habitat requirements. For example, chinook salmon prefer the main channels 

of larger rivers while coho prefer smaller tributaries. 

Of the Section 303(d)-listed parameters in the Stillaguamish, dissolved oxygen, pH, and turbidity 

are the most likely to impair salmon health. Incubation is considered a particularly sensitive lifestage for salmon when adequate instream oxygen concentrations are essential to keep intergravel 

eggs aerated. Most of the salmon species, except for summer steelhead and char, spawn in areas 

that are on the Section 303(d) list for dissolved oxygen. Low pH (below 6.5) becomes a problem 

to salmon in any life stage when it makes metals and other pollutants more reactive and more 

toxic to the fish. Turbidity can reduce salmon spawning habitat when it indicates potential 

siltation of spawning and incubation areas. Elevated turbidities of long duration also can impair 

fish behavior and feeding, and can interfere with gill operation at particularly high turbidities. 
Stillaguamish Fecal and DO TMDL Submittal Report 

Table 8. Stillaguamish River basin water bodies on the 1996 and/or 1998 Section 303(d) list for fecal coliform bacteria, dissopH (Table revised from Ecology July 2004). 

Old ID No. New ID No. Name 1996 Listings 1998 Listings WA-05-1016 QJ28UC Fish Creek Fecal Coliform Fecal Coliform  HD76OJ Harvey Creek Fecal Coliform  JU33JU Jim Creek Fecal Coliform WA-05-1012 GH05SX Jorgenson Slough 

(Church Creek) 

Fecal Coliform Fecal Coliform 

 IJ55EP Lake Martha Creek Fecal Coliform WA-05-1018 VJ74AO Pilchuck Creek Dissolved Oxygen WA-PS-0020 390KRD Port Susan Fecal Coliform Fecal Coliform WA-05-1015 OT80TY 

(Note 1)0.00-2.61 

Portage Creek at 212th St Bridge Fecal Coliform Fecal Coliform, Disso

WA-05-1015 OT80TY 

3.58-8.63 

Portage Creek, several segments including 43rd Avenue Bridge Dissolved Oxygen Dissolved Oxygen 

WA-05-1010 QE93BW Stillaguamish River Fecal Coliform Fecal Coliform, DissoWA-05-1010 ZO73WL Stillaguamish River 

(Hat Slough) 

Dissolved Oxygen Fecal Coliform, Disso

WA-05-1020 WO38NV N.F. Stillaguamish River Fecal Coliform Fecal Coliform WA-05-1050 SN06ZT S.F. Stillaguamish River Fecal Coliform Fecal Coliform WA-05-1040 SN06ZT S.F. Stillaguamish River Fecal Coliform  LU17DC Unnamed Creek #0456 Fecal Coliform DELISTINGS WA-05-1010 QE93BW Stillaguamish River pH (see text page 81) Arsenic (see text page WA-05-1050 SN06ZT S.F. Stillaguamish River Dissolved Oxygen 

(Note 2; text page 80

WA-05-1040 SN06ZT S.F. Stillaguamish River pH (Note 3) pH (Note 3) 

Note 1: Includes the listings mistakenly assigned to QJ28UC, Fish Creek, and YF03BC, a branch of Portage Creek, that sho

OT80TY, Portage Creek. Note 2: Ecology July 2004 TMDL Technical Report: South Fork Stillaguamish above Granite Falls has been meeting standaNote 3: Original pH listing at Arlington (Ecology station 05A090) was based on two samples not meeting standard (two diffe1991); TMDL sampling in 2001 showed no pH values below 6.5 and in summarizing data since 1991, no other occurrences r
Page 28 Stillaguamish Fecal and DO TM

Table 9. Stillaguamish Basin water bodies previously unlisted but found through TMDL to be impaired (revised from Ecology July 2004). ID No. Name Parameter ID No. Name FJ67XF Glade Bekken Fecal Coliform JV77EY Twin City Foods Drain # 1 VJ74AO Pilchuck Creek Fecal Coliform, Dissolved 

Oxygen 

JV77EY Twin City Foods Drain # 2 

WI88QF March Creek Fecal Coliform, Dissolved 

Oxygen 

JV77EY Twin City Foods Drain # 3 

VP67JK Armstrong Creek at Mouth Fecal Coliform WC93GU Twin City Foods Drain # 4 VP67JK Armstrong Creek below 

Hatchery 

Fecal Coliform WC93GU Twin City Foods Drain # 5 

XB43NX Kackman Creek Fecal Coliform, Dissolved 

Oxygen 

SH96KX Warm Beach Creek abov

WWTP 

XF13JD West Pass – Old 

Stillaguamish Channel 

Fecal Coliform SH96KX Agricultural Drain to War

Beach Dike Pond 

UJ01AO South Pass – Old 

Stillaguamish Channel 

Fecal Coliform SH96KX Warm Beach Dike Pond 

AS64WF Douglas Slough Fecal Coliform IE90YH Warm Beach Slough HS19KT Irvine Slough Fecal Coliform QE93BW Stillaguamish River at I-5 GH05SX Church Creek at Park Fecal Coliform WO38NV North Fork Stillaguamish River KX60NO Miller Creek at Miller Road Fecal Coliform SN06ZT South Fork Stillaguamish River 
Stillaguamish Fecal and DO TMDL Submittal Report Page 29

Table 10. General timing of life-stages of Stillaguamish basin salmon species 

(Washington Conservation Commission, 1999) 

Species Life Phase Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec 

Chinook Upstream migration xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 

 Spawning xxxxxxxxxxxxxxxxxx 

 Incubation xxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 

 Juvenile rearing xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 

 Smolt outmigration xxxxxxxxxxxxxxxxxxxxxxx 

Coho Upstream migration xxxxxxxxxxxxxxxxxx 

 Spawning xxxxxxxxxxxx xxxxxxxxxxxxxxxxxx 

 Incubation xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxx 

 Juvenile rearing xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 

 Smolt outmigration xxxxxxxxxxxxxxxxxxxxxxx 

Pink Upstream migration xxxxxxxxxx 

 Spawning xxxxxxxxxxxxxxxxxx 

 Incubation xxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 

 Juvenile rearing xxxxxxxxxxxxxxxxx 

 Smolt outmigration xxxxxxxxxxxxxxxxx 

Chum Upstream migration xxxxxxxxxxxxxxxxxxxxxxxxx 

 Spawning xxxx xxxxxxxxxxxxxxxxxx 

 Incubation xxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxx 

 Juvenile rearing xxxxxxxxxxxxxxxxxxxx 

 Smolt outmigration xxxxxxxxxxxxxxxxxxxxxxx 

Sockeye Upstream migration xxxxxxxxxxxxxxxxx 

 Spawning xxxxxxxxxxxxxxxxxx 

 Incubation xxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxx 

 Juvenile rearing xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 

 Smolt outmigration xxxxxxxxxxxxxxxxxxxxxxx 

Summer Upstream migration xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 

Steelhead Spawning xxxxxxxxxxxxxxxxxxxxx 

 Incubation xxxxxxxxxxxxxxxxxxxxxxxxxxxx 

 Juvenile rearing xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 

 Smolt outmigration xxxxxxxxxxxxxxxxx 

Winter Upstream migration xxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxx 

Steelhead Spawning xxxxxxxxxxxxxxxxxxxxx 

 Incubation xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 

 Juvenile rearing xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 

 Smolt outmigration xxxxxxxxxxxxxxxx 

Char Upstream migration xxxxxxxxxxxxxxxxxxxxxxxx 

 Spawning xxxxxxxxxxxxx 

 Incubation xxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxx 

 Juvenile rearing xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 

 Smolt outmigration xxxxxxxxxxxxxxxxx 

Sea-run Upstream migration xxxxxxxxxxxxxxxxxxxxxxxxxxxxx 

Cutthroat Spawning xxxxxxxxxxxxxxxxxxxxxxx 

 Incubation xxxxxxxxxxxxxxxxxxxxxxxxxxxxx 

 Juvenile rearing xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 

 Smolt outmigration xxxxxxxxxxxxxxxxxxxxxxxx 

 

 

Fisheries specialists have recommended many habitat and channel improvements to assist 

salmon recovery in the Stillaguamish basin (Stillaguamish Technical Advisory Group, 2000). 

Channel sedimentation, increased peak flows, extreme low flows, increased temperatures, and 

reduced dissolved oxygen were identified problems in the basin. The Salmon Habitat Limiting 

Factors Report (Washington Conservation Commission, 1999) for the Stillaguamish basin noted 

that nonpoint sources of pollution such as agricultural practices, on-site sewage disposal, 

development and urban runoff, and forest practices were major causes of water quality problems. 
Page 30 Stillaguamish Fecal and DO TMDL Submittal Report

The Stillaguamish basin attracts many people for recreational opportunities. Salmon fishing is 

one obvious attraction to the river. Boating, riverside picnicking, and swimming occur all along 

the main forks and some tributaries. There are no designated swimming areas with lifeguards 

and bath houses. Full immersion swimming is probably limited to summer periods when air 

temperatures and water temperatures are highest. During the TMDL monitoring surveys, local 

swimming and wading areas were observed on the main branches of the river and on some 

tributaries, at most Washington Department of Fish and Wildlife (WDFW) access areas, public 

parks, and at some bridge crossings. Warm Beach Camp and Kayak Point Regional Park have 

boat launching areas on Port Susan, but no designated swimming areas are present. 

Commercial shellfish harvesting in Port Susan was closed by the Washington State Department 

of Health (DOH) in 1986 due to bacterial contamination. The area became unclassified when no 

commercial interest was taken in the beds, and the DOH stopped monitoring water quality. 

Recreational access for shellfish collection is limited, and the WDFW has recreational harvest 

limits, but none of the beaches have been closed for sanitary considerations under the DOH 

recreational shellfish monitoring program (www.doh.wa.gov/ehp/sf/recshell.htm). 

Water Quality Assessments Since 1998 

The data used for the 1998 Section 303(d) listings were collected from 1988 to 1997 (Ecology, 

2000). Some water quality improvements were in progress by 1997. For example, data collected 

from 1991 to 1994 and analyzed by the Tulalip Tribes (O’Neal, Nelson, and DeNeve, 2001) 

showed only a weak improving trend in fecal coliform counts in the mainstem. By the late 

1990s, improvements were more evident. Joy and Glenn (2000), Klopfer (2000), Thornburgh 

and Williams (2001), and Joy (2001) reviewed and assessed various data sets collected from the 

1980s through 1999. According to their assessments, water quality had significantly improved in 

many parts of the basin, but criteria were not being met in others. Among the findings were the 

following: 

• Fecal coliform (FC) counts at the Stillaguamish River at Interstate 5 had declined 

significantly since 1977. A significant improving step-trend was evident for data collected 

from 1989 to 1993 compared to 1994 through 1999 data. FC data collected from 1995 

through 1999 met both parts of the state water quality criteria. 

 FC counts in Hat Slough at Marine Drive had decreased from 1994 to 1999. However, there 

was still a downstream increase in FC bacteria from the mainstem Stillaguamish River at 

Arlington to Hat Slough. 

 Dissolved oxygen (DO) concentrations were 0.5 – 1.0 mg/L lower at Hat Slough than at the 

Stillaguamish River at Arlington, but none of the concentrations had been below 8 mg/L 

from 1996 to 1999. 

 The Earth Tech (1997) study below the Arlington WWTP demonstrated that diel DO 

concentrations dropped below 8 mg/L (7.2 mg/L) in a pool reach four miles below the 

outfall. Water quality sampling and QUAL2E modeling analyses were performed. 

Periphyton productivity and respiration were the suggested causes rather than effluent 

biochemical oxygen demand or nitrogenous oxygen demand concentrations. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 31

 Church Creek FC counts continued to be elevated throughout the year, but especially during 

storm events. 

 Glade Bekken, formerly Tributary 30, was monitored by Snohomish County during a 

watershed restoration project. FC counts had decreased in the creek, but did not meet 

criteria. DO concentrations have met the Class A criterion. 

 Portage Creek continued to have low DO concentrations that do not meet the Class A 

criterion during low-flow periods, and elevated FC counts that do not meet criteria 

throughout the year. 

 Pilchuck Creek DO concentrations have improved since 1995, and none of the concentrations 

through 1999 had been below 8 mg/L. 

• FC data collected by Ecology from the South Fork Stillaguamish River at Arlington from 

1995 through 1999 met both parts of the state water quality criteria. 

• DO concentrations from the South Fork Stillaguamish River at Arlington have not been 

below 8 mg/L from 1995 through 1999, and no pH violations have been observed in the data 

since 1990. 

• A 1995 step trend was evident that showed decreasing FC counts in the North Fork 

Stillaguamish River at Cicero. FC counts met Class A criteria. 

• FC counts were in compliance with Class AA criteria in 1999 at both the North Fork at 

Darrington and at the South Fork at Granite Falls. 

• The Stillaguamish Tribe has been sampling FC at several sites in northern Port Susan since 

summer 1998 (Klopfer, 2000). Most sites have shown slight improvements through 1999. 

Sites nearest to Hat Slough were not meeting marine water DOH FC criteria. The sites south 

(Warm Beach Point and Kayak Point) and the sites to the northwest (North Port Susan and 

Peripheral Site 4) appeared to be within DOH FC criteria. The site near Warm Beach Slough 

has experienced the worst bacterial water quality of the sites monitored. 

Fecal coliform counts and dissolved oxygen and ammonia concentrations in the basin have been 

improving in several areas. Some of these improvements may have coincided with the federal 

Dairy Buyout Program in the mid-1980s that reduced the number of cows in most Puget Sound 

basins. Many more of the improvements reported through the 1990s coincide with 

implementation of the Stillaguamish Watershed Plan and work implemented by the 

Stillaguamish Clean Water District. 

In 1987, Ecology selected the Stillaguamish River basin as one of six “Early Action Watersheds” 

in the Puget Sound basin. As such, a watershed management committee was formed and 

received grant money to write the Stillaguamish Watershed Action Plan. The 1990 plan and 

accompanying technical supplement addressed the magnitude of various nonpoint sources of 

pollution and the actions needed to control and prevent problems from those sources. 

The Stillaguamish Clean Water District Board, the Stillaguamish Implementation and Review 

Committee, and the Flood Control District continue to direct and fund implementation of the 

tasks stated in the action plan, and respond to newer concerns for salmon habitat restoration. 

Snohomish County Surface Water Management, Snohomish Conservation District, the 
Page 32 Stillaguamish Fecal and DO TMDL Submittal Report

Stillaguamish Tribe, the Tulalip Tribes, and other local groups have been working together to 

improve water quality by controlling and preventing nonpoint sources in the Stillaguamish basin 

and in Port Susan. 

Analytical Framework 

The technical analysis of the data for this TMDL required the use of several mathematical 

procedures, mathematical models, and statistical equations. Some of the procedures and 

equations were used for all of the parameters examined; others were used only for specific 

parameters. 

The following section describes the analytical processes used for each parameter and any 

accompanying assumptions needed for the procedures. The procedures used to establish critical 

conditions and to evaluate seasonal variability are also described. The procedures, assumptions, 

and rationale create the technical framework that supports the findings and conclusions in 

Technical Analysis and Loading Capacity sections of this report. 

Fecal Coliform 

The Stillaguamish River basin has an extensive data set on which to evaluate historical and 

current bacterial conditions, establish trends, and identify critical conditions: 

• The fecal coliform (FC) data at enough key freshwater sites are from long-term (greater than 

ten years) monitoring programs so that trends can be determined. 

• The sampling at these sites has been monthly and random without bias to climatological or 

hydrological events. 

• The basin is not under any manipulations from diversions or damming. Therefore, the 

distribution of FC counts should represent the major factors affecting FC counts at a 

particular site: source strength, dilution, die-off, and dispersion. 

• The cumulative FC counts at most sites follow a lognormal distribution. 

The attributes of this data set are ideal for using the Statistical Rollback Method (Ott, 1995). The 

method is used to determine if FC distribution statistics for individual sites meet the water 

quality criteria in the Stillaguamish River basin. The method has been successfully applied by 

Ecology in other FC bacteria TMDL evaluations (Cusimano and Giglio, 1995; Pelletier and 

Seiders, 2000; Coots, 2002). 

Briefly, the geometric mean (approximately the median in a lognormal distribution) and 

90th percentile statistics are calculated and compared to the FC criteria. If one or both of the 

population statistics do not meet the criteria, then the whole distribution is “rolled-back” to 

match the more restrictive of the two criteria. The 90th percentile criterion usually is the most 

restrictive. The new geometric mean and 90th percentile statistics then becomes the “target” 

statistics for the site. (The term target is used to distinguish these estimated numbers from the 
Stillaguamish Fecal and DO TMDL Submittal Report Page 33

actual water quality criteria.) The amount a distribution of FC counts is “rolled-back” from the 

original statistics to the most restrictive criterion, and target statistic is calculated as the percent 

of FC reduction required to meet the FC loading capacity. A detailed graphical example and 

interpretation is shown in Appendix B. 

The rollback was applied to the most representative distribution after taking several analytical 

steps. Both step trends and monotonic trend analyses were performed on FC counts and 

discharge volumes to determine the most recent and stable data set, i.e. to ensure that high water 

and drought years are represented equally. Trend analyses, tests for seasonality, and statistical 

tests for lognormal distributions were performed using WQHYDRO, a statistical software 

package for environmental data analysis (Aroner, 2001). The geometric mean and 90th percentile 

statistics for various subsets of data were then calculated and compared to determine a critical 

season at each site, and to determine the target statistics. 

Port Susan FC data were evaluated using the 30-day running average and 90th percentile 

statistical analysis required by the Food and Drug Administration for commercial shellfish 

harvest areas. The statistical formula for deriving the 90th percentile is shown in Appendix B. 

Data were also evaluated to determine if a seasonal component was evident. The FC count 

comparisons between sites on an event basis and location of sites relative to the mouths of the 

Stillaguamish River (Hat Slough and South Pass) were investigated using regression analyses. 

FC field data collected during the September 2000 synoptic survey were used to calibrate the 

QUAL2Kw model for the lower Stillaguamish River (Arlington to Hat Slough). The model 

simulations of the September survey were helpful to: 

• Characterize conditions of low dilution potential for FC point and nonpoint sources. 

• Evaluate the relative impact of FC loading from monitored tributaries and point sources to 

the lower mainstem. 

• Reveal residual loads from unidentified sources. 

• Compare current FC loading from point, tributary, and nonpoint sources to simulations after 

recommended target FC reductions on those sources are achieved. 

Pelletier and Bilhimer’s (2004) QUAL2Kw model for the Stillaguamish Basin Temperature 

TMDL provided the channel and flow foundation on which to include additional parameters for 

analysis. A detailed discussion of how local channel morphology, basin hydrology, and 

climatological data were incorporated into the model is found in Pelletier’s (2003) report. 

Bacteria counts were simulated in QUAL2Kw using the pathogen function (Chapra, 2001; 

Pelletier and Chapra, 2003). The model subjects bacteria input to die-off and settling. Die-off is 

a function of light exposure and a chosen temperature-dependent natural loss rate. The light’s 

killing effectiveness is a function of the intensity of the sunlight, atmospheric factors like clouds 

and haze, and the clarity and depth of the water. Losses by settling depend on the settling 

velocity chosen and the depth and velocity of the water. 

FC loading estimates from tributaries, point sources, and nonpoint sources were accomplished by 

first completing a flow balance for the lower mainstem. As part of the QUAL2Kw modeling, 

Pelletier and Bilhimer (2004) had calculated flow balances for the 2000-2002 TMDL study 
Page 34 Stillaguamish Fecal and DO TMDL Submittal Report

period. Flow balances were estimated from field measurements and gage data of flows made by 

Ecology and the USGS, and weighted by annual average precipitation according to the subwatershed areas. A flow balance spreadsheet of the stream networks for the Stillaguamish River, 

South Fork Stillaguamish River, North Fork Stillaguamish River, Deer Creek, and Pilchuck 

Creek was constructed to estimate surface water and groundwater inflows by interpolating 

between the gauging stations. 

Since discharge records are lacking for the lower 17 kilometers of the Stillaguamish River and 

the Old Stillaguamish Channel, an assumption was made that on average ten percent of the 

discharge in the Stillaguamish River is diverted to the Old Channel. Further assumptions were 

made that the Old Channel flow increases 2.5 percent from Church Creek and other drainage 

areas before half of the Old Channel is discharged through South Pass to Port Susan and the 

other half through West Pass to Skagit Bay. 

FC loads from Hat Slough and South Pass were estimated using an unbiased stratified ratio 

estimator equation from Thomann and Mueller (1987). The formula for the equation is shown in 

Appendix B. Annual, monthly, and seasonal FC loads were calculated from estimated discharge 

volumes at Interstate 5 and FC counts collected at Hat Slough and South Pass by staff from 

Ecology, the Stillaguamish Tribe, and Snohomish County Surface Water Management. 

FC loads from seals and birds were also estimated and compared to the Stillaguamish River 

loads. Seal FC loading estimates were based on average rates from Puget Sound studies 

(Calambokidis, McLaughlin, and Steiger, 1989) and from seal population estimates provided by 

the National Marine Fisheries Marine Mammal Program. Bird FC loads were estimated from 

Audubon bird counts in the Port Susan area (Cullinan, 2001), and from literature FC generation 

values for domesticated birds (ASAE, 1998). 

FC loads in stormwater are generated from a variety of sources. Data collected over the past 

40 years have suggested that these sources vary in intensity and are often generally associated 

with certain land uses. In the past few years, stormwater-generated pollutants have come under 

closer scrutiny by regulating authorities. Certain jurisdictions are now being held responsible for 

the quality and quantity of stormwater discharged by their systems under the federal Clean Water 

Act. 

In 2002, a directive came from EPA requiring all TMDLs in jurisdictions with NPDES permits 

for stormwater systems to include the pollutant loads from those systems as wasteload 

allocations (Wayland and Hanlon, 2002). The directive came after sampling was completed for 

the Stillaguamish Basin TMDL, but Snohomish County and the Washington State Department of 

Transportation (WSDOT) have Phase I NPDES permits for their stormwater systems. Arlington 

and Granite Falls have submitted applications for stormwater permits under Phase II. 

Data were not collected during the TMDL study to specifically characterize the storm water from 

these NPDES permit sources. To comply with the EPA directive, stormwater FC loads from the 

five jurisdictions were estimated using the ‘Simple Method Model’ (Stormwater Center, 2004). 

The model requires the sub-basin drainage area and impervious cover, stormwater runoff 

pollutant concentrations, and annual precipitation. The land uses in each sub-basin were 
Stillaguamish Fecal and DO TMDL Submittal Report Page 35

categorized as residential, commercial/industrial, agricultural, forest, and roadway. FC loads 

were calculated for each category to judge its relative importance to FC loading. 

The model equations are presented in Appendix B. Data inputs were obtained from Geographic 

Information System covers depicting land use types, road densities, drainage areas, and annual 

precipitation volumes. Estimates of pollutant concentrations for various land use types were 

taken from literature sources (Stormwater Center, 2004; Novotny and Olem, 1994; National 

Stormwater Database, 2004; Embrey, 2001). 

Snohomish County and WSDOT wasteload allocations were based on the contribution of each 

jurisdiction to the “Roadway” category. Conveyance of contaminants from adjacent land uses to 

the roadway ditches was not considered for this level of analysis. In contrast, municipal 

stormwater wasteload allocations were based on all land use categories within the urban 

boundary, not just the Roadway category. State highways through municipalities were 

subtracted from the municipal area and counted towards the WSDOT Roadway area. 

When NPDES permits are reissued, wastewater treatment plants with permits will have new 

effluent discharge limits based on the wasteload allocations established in this TMDL. Based on 

the EPA guidance (Wayland and Hanlon, 2002), NPDES stormwater permit holders will not be 

issued numeric effluent limits as a result of wasteload allocations set in this TMDL but rather 

will be expected to address the requirements through adoption of Best Management Practices 

(BMPs). 

Dissolved Oxygen 

Most dissolved oxygen (DO) data collected in the Stillaguamish River basin have been from 

instantaneous daytime ‘grab’ measurements during daytime hours. Seven freshwater areas were 

on the 1998 303(d) list based on data collected in this way. Since minimum DO concentrations 

in productive systems often occur before dawn, it is difficult to interpret these data in terms of a 

state criterion stated as a minimum concentration that is consistently to be exceeded (Table 6). 

Trend analyses also become more difficult if the time of day when samples were collected 

shifted between blocks of years. 

Taking multiple grab samples over the course of a day is one approach to estimate the diel range 

of DO concentrations. This can be very resource intensive in a large geographic area. 

Continuously recording DO probes deployed over a few days is another solution to the problem. 

This method was used at a limited number of sites because of the limited availability of the 

equipment. 

Without extensive data, the relative contribution of natural and anthropogenic sources to areas 

with depressed DO conditions becomes difficult to assess. The low DO concentrations could be 

related to factors other than excessive instream productivity, e.g., riparian wetlands, stormwater 

discharges, and low DO groundwater input. 

A multiple-step approach was taken to evaluate the instantaneous DO measurements collected at 

36 freshwater sites. The lowest set of DO data at each site were referenced to season, time of 
Page 36 Stillaguamish Fecal and DO TMDL Submittal Report

collection, flow, and accompanying temperature, pH, and nutrient data. Field observations were 

also taken into account. Sites were then divided into two categories: 

1. DO data from high productivity systems: DO measurements collected during the growing 

season and under lower flow conditions with accompanying pH values above 7, and nutrient 

concentrations seasonally influenced by excessive biomass production. 

2. DO data from systems influenced by other factors: DO measurements collected throughout 

the year with accompanying pH values less than 7, and nutrient concentrations less 

seasonally variable. 

Low DO concentrations from the first group were evaluated according to Ecology TMDL 

guidelines by adding a 0.5 mg/L safety factor to the water quality criterion (TMDL Workgroup, 

1997). The criterion plus safety factor was compared to the lowest 10th percentile DO value 

reported over the most representative period of record. For example, the lowest allowable 

10th percentile concentration for a Class A water would be 8.5 mg/L, as applied to the 

instantaneous measurements collected over the period of record. The rank 10th percentile value 

was calculated using the EXCEL® percentile formula (Appendix B). The safety factor allows 

for the likelihood that DO values recorded during daylight hours are higher than those existing 

before dawn because of instream productivity. The rank 10th percentile value was chosen to 

represent the average daily DO concentration during critical conditions for a particular site. 

The second group of sites required more site-specific judgments about the ability of the water 

body to meet the criterion and beneficial uses. Fish habitat, soils, ground water quality, and 

wetlands data were reviewed. At these sites, anthropogenic source loadings of biochemical 

oxygen demand (BOD) were estimated using the Simple Method Model (Stormwater Center, 

2004) results based on land use types in the sub-basin, relative to potential natural sources of 

low DO water like ground water or wetlands. Fecal coliform counts and other water quality 

data were considered for the pollutant loading assessments, so stormwater BOD wasteload 

allocations and background load allocations, as well as estimates of BOD load capacities, 

were based on the fecal reductions required to meet criteria. 

 

Two point sources discharge to receiving waters identified as having potential DO limitations 

due to natural conditions; i.e., the DO minimum concentrations are naturally lower than the state 

DO criterion. Effluent from the Warm Beach Conference Center wastewater treatment plant 

(WWTP) currently discharges to Warm Beach Creek. Arlington WWTP discharges to the 

mainstem Stillaguamish River below the confluence of the North and South forks. As explained 

in the Applicable Water Quality Criteria section, anthropogenic source discharges are not 

allowed in areas that would further decrease DO concentrations more than 0.2 mg/L, so 

additional data analyses were conducted at these two sites. 

NPDES permit limits for BOD loads and ammonia (for nitrogenous oxygen demand) were 

evaluated for direct oxygen loss potential from both WWTPs in the two receiving waters. 

Effluent total nitrogen and phosphorus concentrations were also assessed as part of the 

Arlington WWTP impact assessment. The Arlington WWTP assessment required detailed 

critical condition determinations and modeling. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 37

Diel DO on the mainstem Stillaguamish River from the confluence of the North and South forks 

to Hat Slough was evaluated to analyze the impact of Arlington WWTP effluent on downstream 

reaches of the river. The QUAL2Kw model (Chapra, 2000) as modified by Pelletier (Pelletier 

and Chapra, 2003) was calibrated to the mainstem DO conditions observed during the three-day 

October 2001 TMDL survey. This set of survey data contained the following: 

• Nutrient and field parameter measurements at nine sites on the mainstem from the confluence 

of the forks to Hat Slough, and sample analyses and field measurements from Arlington 

WWTP and four tributaries. 

• Continuous DO, temperature, pH, and conductivity probe measurements taken at four sites in 

the reach (Figure 7). 

• Periphyton biomass measurements at three sites. 

Figure 7. Locations of four diel monitoring probes (broad crosses) in the Stillaguamish River from 

Arlington to Interstate 5 in September 2000 and October 2001. RKM = river kilometer 

Arlington 

WWTP 

Stillaguamish Rive

Portage Creek

Armstrong Creek

Interstate 5 

RKM 17.7 

RKM 21.7

RKM 

24.0 

RKM 

28.5

March Creek
Page 38 Stillaguamish Fecal and DO TMDL Submittal Report
Stillaguamish Fecal and DO TMDL Submittal Report Page 39

The August 1997 survey by Earth Tech (1997) was used for model verification. The data set was 

much more limited, but the survey was conducted during a low-flow event close to what would 

be considered critical conditions (See Technical Analysis: Dissolved Oxygen, Critical 

Conditions). 

The diel DO output in QUAL2Kw is affected by DO saturation, re-aeration, photosynthetic and 

respiration processes, and carbon and nitrogen oxidation. DO saturation is calculated from 

temperature and barometric pressure. Several re-aeration formulas are available in the model 

that are automatically selected depending on depth and velocity ranges of a reach. 

Photosynthesis and respiration functions for periphyton, and heterotrophic bacteria respiration in 

the hyporheic zone were incorporated into this version of the model by Pelletier (Pelletier and 

Chapra, 2003). The modifications to the QUAL2Kw model are detailed in Appendix C. 

The model was set up to run critical conditions, and the results were compared to Class A 

criteria. The critical condition simulations included: 

River discharge set to the estimated lowest seven-day average flow with an annual ten-year 

recurrence interval (7Q10) volume assuming a stabilized channel and biological condition, i.e., 

no spates during the previous 30 days that would scour periphyton and heterotrophic bacteria 

biomass. 

• Upstream temperature, pH, and nutrients set at seasonal 90th percentile values, and DO and 

alkalinity set at seasonal 10th percentile values. 

• Arlington WWTP discharge rates and effluent characteristics set to dry season maximums for 

Phase 1 and Phase 2 expansions (Earth Tech, 1996). 

• Benthal or groundwater oxygen demand, or hyporheic exchange active in pool reaches. 

• Periphyton biomass volumes set at highest levels observed in 2001. 

Simulations with and without point sources and suspected nonpoint sources, and with modified 

headwater characteristics, were compared. The pollutant load capacity for the Stillaguamish 

River was determined for compliance with DO standards after evaluating the various simulations 

(see Loading Capacity). 

pH 

The pH measurements taken in the basin create the same difficulty as the dissolved oxygen 

measurements for comparison to the state criteria; i.e., the instantaneous measurements do not 

necessarily account for diel maximum and minimum values in productive systems. In addition, 

low pH values in the basin appear to occur during stormwater events or in certain hydrologic 

environments, while high pH may be related to biomass production during low-flow events. 

Only the South Fork Stillaguamish River was on the 303(d) list for pH violations (less than 6.5), 

but other potential candidates were documented after evaluating data from 27 sites for this 

assessment (see Technical Analysis and Loading Capacity). 

Instantaneous pH measurements were assessed in a manner similar to the dissolved oxygen 

measurements. The pH data at all sites were reviewed in the context of other factors like season, 
Page 40 Stillaguamish Fecal and DO TMDL Submittal Report

time of collection, and dissolved oxygen and nutrient concentrations. In addition, monitoring 

site locations were inspected to determine if upstream wetlands and groundwater influences were 

possible. Sites were separated into two groups: 1) those with potential high or low pH criteria 

violations from excessive instream productivity, and 2) those with low pH values potentially 

related to other factors. 

Although diel pH variability is not specifically addressed in the Ecology TMDL guidelines 

(TMDL Workgroup, 1997), the safety factor approach is reasonable for the first group of sites. 

In a biologically productive stream or river, the diel pH range can be determined by influences of 

instream respiration and productivity on the water carbonate buffering capacity. From the diel 

data that are available from the mainstem surveys, a safety factor of 0.2 standard units (s.u.) was 

chosen to cover the maximum diel range observed during TMDL surveys. The safety factor was 

applied to the 10th and 90th percentile pH for each site. The rank 10th and 90th percentile statistics 

were calculated using the EXCEL® percentile function (Appendix B). For example, sites located 

in Class A and Class AA waters in the first group with a rank 90th percentile pH value greater 

than 8.3, or a 10th percentile value less than 6.7 were considered threatened. Water quality 

standards for Class A and AA waters require pH values between 6.5 and 8.5 s.u. (Table 6). 

In the Stillaguamish basin, depressed rather than elevated pH values were more common at 

several sites. These sites also had low pH values at mid-day rather than in the early morning. 

Therefore, the diel pH range is probably not a function of instream productivity as much as from 

groundwater input or decomposition processes from upstream wetlands. At these sites, potential 

anthropogenic sources of depressed pH are listed and their impact estimated after reviewing and 

evaluating fecal coliform, biochemical oxygen demand, and nutrient data. The impact is 

compared to a range of groundwater pH values (Thomas, Wilkinson, and Embrey, 1997) or other 

data from the area. 

 

Arsenic and Mercury 

Arsenic and mercury in the Stillaguamish River and two forks were assessed as concentrations 

and as loads based on six or more sampling events at four sites during the 2000-2002 TMDL 

study period (See Technical Analysis: Arsenic and Mercury). Additional arsenic data within the 

study period was also obtained for two sites in the basin from another Ecology study (Johnson, 

2002). Concentrations of the two metals were compared to criteria (Table 6). Event arsenic and 

mercury loads were evaluated to identify potential sources. Discharge estimates for the load 

calculations were based on USGS gauging data and Pelletier’s (2003) water balance work 

described earlier. The loads of both metals were compared to each other and to total suspended 

solids loads using regression analyses to evaluate correlations and transport mechanisms. 

Seasonal Variation and Critical Conditions 

Clean Water Act Section 303(d)(1) requires that TMDLs be established at level necessary to 

implement the applicable water quality standards with seasonal variations. The current 

regulation also states that determination of TMDLs shall take into account critical conditions for 

stream flow, loading, and water quality parameters [40 CFR 130.7(c)(1)]. Finally, Section 

303(d)(1)(D) suggests consideration of normal conditions, flows, and dissipative capacity. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 41

The parameters and some geographic areas being evaluated in this Stillaguamish TMDL have 

different critical conditions and seasonal variations. The critical conditions for elevated fecal 

coliform counts and loads are different from the conditions when low dissolved oxygen 

concentrations are reported. In addition, the sources of fecal coliform contamination vary, so the 

critical condition for fecal coliform in the mainstem is different from the condition in some 

tributaries. 

The data records were evaluated to identify critical conditions for each parameter at specific 

sites. For example, trend analyses, tests for seasonality, and statistical tests for lognormal 

distributions were performed using WQHYDRO, a statistical software package for 

environmental data analysis (Aroner, 2001). Regression analyses were performed to test if 

various pollutants of concern were correlated with each other, with discharge volumes, with total 

suspended solids, or with climatological events. To simplify implementation of the TMDL, an 

attempt is made to define the critical condition in common to as many sites as possible for a 

parameter like fecal coliform or dissolved oxygen without jeopardizing beneficial uses at any 

specific site in the basin. 

Technical Analysis 

This Technical Analysis section describes and presents analyses of the most recent data to 

establish the current water quality conditions in the basin, especially in those areas and for those 

parameters on the 1998 303(d) list (Table 1). The hydrological and climatological characteristics 

are first described under which the recent water quality data were collected. Then the results of 

fecal coliform, dissolved oxygen, pH, and arsenic and mercury sample data are discussed using 

the methods previously described in the Analytical Framework section of this report. The 

critical conditions determining the loading capacities and TMDLs for each parameter are also 

described. 

Data from several sources were combined to evaluate the current state of water quality in the 

Stillaguamish basin and Port Susan. Data from Ecology surveys conducted from 2000 to 2001 

under the TMDL quality assurance project plan have been reviewed for their acceptability and 

published (Coffler, Gridley, and Joy, 2004). Quality assurance plans were in place for the 

2000 to 2002 Snohomish County, Stillaguamish Tribe, and Ecology ambient monitoring 

programs. The collective database represents four types of monitoring to characterize different 

aspects of contaminant sources and transport mechanisms: 

• Long-term data collection from the networks established over the past 30 years by Ecology, 

the Tulalip Tribes, the Stillaguamish Tribe, Snohomish County Surface Water Management, 

and the NPDES permit program. 

• Medium-flow and storm-event synoptic sampling in 2000 and 2001 (Figure 8). 

• Enhanced monthly sampling in 2001 in Port Susan and key tributaries based on the 

Stillaguamish Tribe Port Susan and tributary network (Figure 9). 
Page 42 Stillaguamish Fecal and DO TMDL Submittal Report

• Short-term weekly monitoring of informal recreational beaches in summer 2000 (bacteria 

only). 

The location and some data analyses of the long-term network sites and recreational beach sites 

were previously described and discussed in pre-TMDL work (Joy and Glenn, 2000; Joy, 2001). 

Current data are defined as samples and measurements taken from June 2000 through June 2002. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 43

#Y

#Y

#Y

%U

% %U U

%U%U%U

%U %U %U%U

%U%U%U %U %U

%U %U %U %U %U %U %U %U %U %U %U%UU%U %U %U %U

%U %U %U

%U

%U

%U%U

%U

%U

%U%U%U

%U

%U

%U

%U

%U

%U%U %U

Pilchuck Creek

Portage Creek

Old Channel

Hatt Slough Glade Bekken

Harvey Creek

Armstrong Creek

South Fork Stillaguamish River

North Fork Stillaguamish River

Arlington

Stanwood

Granite Falls

Warm Beach

N

W E

S

South Fork

North Fork

Pilchuck Creek

Main Stem

Monitoring Site

Stillaguamish River

%U

Figure 8. Water quality monitoring sites in the Stillaguamish River basin used by 

 Ecology for storm-event and synoptic surveys.
Page 44 Stillaguamish Fecal and DO TMDL Submittal Report

Figure 9. Fecal coliform monitoring sites located in and around northern 

Port Susan. Circles are sites monitored by the Stillaguamish Tribe; triangles 

are sites monitored by Ecology. 

Flows and Rainfall 

According to records from the Arlington Airport, the TMDL surveys took place during a wetter 

than normal summer season in 2001, and drier than normal fall season in 2000. Annual rainfall 

at Arlington was 39.55 inches in 2000, and 50.05 inches in 2001. The average rainfall over 40 

years of complete records is 46.83 inches. The lowest annual rainfall, 30.3 inches, was recorded 

in 2002. 

The 2001 water year (October 2000 through September 2001) was among the lowest on record 

for river discharge (Table 11). The lowest annual mean daily flow was 1123 cfs in 1930, and the 

highest was 2883 cfs in 1997. The months of October through May had lower than average 

monthly flows. The 90th percentile average daily peak flows for water year (WY) 2000 and WY 

2001 are low compared to 3720 cfs for the period of record. The North Fork mean daily 

discharge exceeded 3720 cfs on only seven days in WY 2001, and on only 17 days through the 

2000-2002 TMDL study period. In contrast, both annual seven-day average low-flows for 2000 

and 2001 were higher than the period of record’s seven-day average, ten-year, low-flow statistic 

PS4-130 

PS2-128

N. Port Susan126 

PS8-140 

PS7-139 PS9-148 

PS5-137 

PS6-138 

PS3-129 

S. Branch Pilings-123

Warm Beach Pt.-124

West Branch-121

South Branch-122

Juniper Beach 

South Pass

Twin City # 1

Twin City # 4 (170)

Hat Slough - 120

Lake Martha Cr. (067)

Unnamed Cr # 0456

Warm Beach Slough - 127

Warm Beach Sites

Stanwood Camano Island

Stillaguamish River

Lake Martha

Old Stillaguamish Channel

Port Susan 

Kayak Point - 125 
Stillaguamish Fecal and DO TMDL Submittal Report Page 45

(7Q10) of 175 cfs. The annual seven-day low-flow is the lowest mean value for any seven 

consecutive day period between October 1 and September 30. 

Table 11. Flow statistics for the North Fork Stillaguamish River near Arlington 

(USGS 12167000) comparing period of record data to water years 2000 and 2001. 

Annual 

average 

7-day average 

low-flow 

90th percentile 

Period of record high-flow 

cms (cfs) cms (cfs) cms (cfs) 

1928 – 2001 53.58 (1892) 4.96 (175)* 105.4 (3720) 

Water year 2000 53.35 (1884) 7.96 (281) 99.4 (3510) 

Water year 2001 33.22 (1173) 7.22 (255) 59.8 (2110) 

* The seven-day, ten-year, low-flow statistic for the period of record 

The discharge of the Stillaguamish River at the I-5 bridge was estimated from the North Fork 

Stillaguamish gage record using multiple regression techniques. The estimated annual daily 

average discharge at I-5 was 2433 cfs for WY 2001. The estimated seven-day average low flow 

in WY 2000 was 602 cfs, and in WY 2001 it was 547 cfs; both occurred in late September. The 

general response of river discharge to rainfall over the TMDL study period is shown in 

Figure 10. 

One feature, a late-August storm in 2001, is quite prominent in the gauge record. The storm 

dropped 0.65 inches over three days and increased the estimated mean daily discharge from 524 

cfs prior to the storm, to 5895 cfs at the peak of runoff. The storm scoured the riverbed during 

the active benthic algae growing period, and sent a pulse of poor quality water into Port Susan. 

A range of flow and climatological conditions were monitored. A mid-range flow synoptic 

survey was conducted on September 11-13, 2000. The mean daily discharge at I-5 was 

estimated at 2100 cfs on the first day after a total rainfall of 0.19 inches over the previous five 

days. The discharge at I-5 steadily dropped to 1010 cfs on the third day. A low-flow survey was 

conducted on October 2-4, 2001 with fairly stable, but slightly dropping, flows at I-5 of 590 cfs – 

530 cfs. A late-spring storm event was monitored on June 12-13, 2001 with mean daily flows of 

6280 cfs and 4210 cfs during a two-day cumulative rainfall of 1.27 inches. The five-day 

antecedent precipitation measured 0.01 inches. A mid-fall storm was monitored on November 

14-15, 2001 with a two-day cumulative rainfall of 0.64 inches, and a five-day antecedent rainfall 

of 0.05 inches. Mean daily flows at I-5 were estimated at 19,020 cfs and 15,340 cfs. 
Page 46 Stillaguamish Fecal and DO TMDL Submittal Report
Stillaguamish Fecal and DO TMDL Submittal Report Page 47

100

1000

10000

100000

Mar-00 May-00 Aug-00 Nov-00 Feb-01 May-01 Aug-01 Nov-01

Date

Discharge (cfs)

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

Daily Rainfall (inches)

<------------------------------------ TMDL Survey Events ------------------------------->

Figure 10. Estimated discharge record for the Stillaguamish River near Silvana 

 (continuous line) and daily rainfall (vertical spikes) recorded at Arlington Airport 

 during Ecology’s TMDL surveys, July 2000 to November 2001. 

Fecal Coliform 

Current Conditions and Trends 

Fecal coliform (FC) counts and loads in the 2000 – 2001 TMDL sampling period at some sites 

were more variable than in previous years. Data from the Stillaguamish River at Interstate 5 (I5) are typical (Figure 11). FC data at I-5 collected in the 2001 water year, when most sampling 

took place, had a lower than usual median count and load, but a higher than usual 75th percentile 

and maximum count. The wetter than normal summer and fall of 2001 and drier than normal fall 

of 2000, along with a low water year in 2001, probably exerted an influence on the increased 

variability in FC run-off, but resulted in a lower median FC load at I-5. Some of the apparent 

increases at other sites can be explained as database artifacts from more intensive monitoring 

activity, especially with the inclusion of storm-event data. However, FC count and load 

increases appeared to carry through to the 2002 water year at I-5 (Figure 11), when monitoring at 

other sites returned to routine sampling intervals. 

 
Page 48 Stillaguamish Fecal and DO TMDL Submittal Report
Stillaguamish Fecal and DO TMDL Submittal Report Page 49

Elevated FC counts in 2001 were responsible for interrupting improving trends at several sites. 

The Stillaguamish River at I-5, North Fork Stillaguamish River at Cicero, Pilchuck Creek, 

Stillaguamish River at Hat Slough, Stillaguamish River below Arlington, South Fork 

Stillaguamish River at Arlington, and Armstrong Creek below the Hatchery had decreasing 

FC bacteria trends since the mid-1990s that were all negatively affected by poor bacterial water 

quality during the TMDL survey years. For example, data collected three to five years before 

and after 1998 at the South Fork Stillaguamish River at Arlington suggested there was a 

statistically significant decline in FC counts (Figure 12 – lower graph). There was no longer a 

statistically significant difference after including counts from 2001 (Figure 12 – upper graph). 

Despite the increases in 2001 FC counts, water quality criteria were met most of the time at sites 

along the mainstem and forks. FC counts in the upper North and South forks continued to be 

well within FC criteria during all sampling surveys. The elevated FC counts observed in the 

1990s at several sites along the upper North Fork that were responsible for the 303(d) listings of 

those reaches did not occur during the 2000-2002 TMDL study period. Some of the sources 

causing bacteria contamination may have been eliminated from those reaches. Usually water 

quality in the mainstem below the confluence of the forks was well within the Class A FC 

criteria. Elevated counts occurred only after significant storm events. The influence of these 

events will be discussed later in this report (see next section, Synoptic Surveys and Storm 

Events). 

Several tributaries on the 1998 303(d) list for FC criteria violations continued to be out of 

compliance with standards based on the TMDL survey data. Trend analyses suggested that Fish 

Creek and Jim Creek had shown improvement over previous years, while Harvey Creek, 

Jorgenson Slough (Church Creek), Lake Martha Creek, Portage Creek, and Unnamed Creek had 

experienced no change or appeared to be worse. Of these smaller tributaries on the 303(d) list, 

only Jim Creek met FC criteria based on data collected in 2000 – 2001. 
Page 50 Stillaguamish Fecal and DO TMDL Submittal Report cfu/100 mL

WATER YEAR

 1

10

 100

1000

 10000

95 96 97 98 99 00 01 02

WQ Standard 

WQ Standard 

(12) (12)

(11)

(12)

(12)

(12)

(12)

(10)

FC Load 

WATER YEAR

 10000

100000

 1000000

10000000

 100000000

1000000000

95 96 97 98 99 00 01 02

(12)

(12) (11)

(12)

(12)

(12)

(12) (10)

Figure 11. Fecal coliform count and estimated load (cfu/day x 106) statistics for monthly samples 

 collected from the Stillaguamish River at Interstate 5 (Ecology Station 05A070) for water years 1995 to 

 2002. Class A FC criteria are indicated in the upper figure. The box-plot depicts the median, 10th, 25th, 

75th, and 90th percentiles, and the range. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 51 Fecal coliform (cfu/100 mL) 

YEAR

SF Stillaguamish at Arlington 

Step Trend '94-'98 and '99-'02

 1

 2

10

20

 100

 200

1000

94 95 96 97 98 99 00 01 02

 Y = -4.500

NOT Signif 80%

2xP = 0.2553 

S.Wilcoxon-Mann-Whitney Test

& S.Hodges-Lehmann Estimator

WQ Standard 

WQ Standard 

Fecal coliform (cfu/100 mL) 

YEAR

 1

 2

10

20

 100

 200

1000

94 95 96 97 98 99 00 01 02

 Y = -8.000

Signif 95%

2xP = 0.0112 

S.Wilcoxon-Mann-Whitney Test

& S.Hodges-Lehmann Estimator

WQ Standard 

WQ Standard 

Figure 12. Two graphs of data from the South Fork Stillaguamish River that 

 show the influence of the 2000-2001 monitoring year on Stillaguamish fecal 

coliform statistical trends (see text). 
Page 52 Stillaguamish Fecal and DO TMDL Submittal Report

Other tributaries, not on the 303(d) list, were identified with FC criteria violations based on the 

TMDL data set. These included Glade Bekken, Miller Creek, Warm Beach Creek including the 

Pasture Drain and pond, Douglas Slough, Irvine Slough, Pilchuck Creek, March Creek, 

Kackman Creek, and several drains near Port Susan. 

Port Susan Area 

Port Susan was added to the TMDL study area in 2001 (Joy, 2001). Port Susan coliform data 

collected by the Stillaguamish Tribe exhibited an increase at sites in 2001 after showing 

improvements between 1998 and 2000. The Washington State Department of Health (DOH) 

Food Safety and Shellfish Programs uses 30-sample running geometric means and 90th percentile 

statistics to judge the suitability of bacteriological water quality in commercial shellfish harvest 

areas (Appendix B). The DOH only uses the most probable number (MPN) type of FC analysis 

to calculate the statistics (see Applicable Water Quality Criteria). These statistics appeared to be 

coming within the acceptable criteria (a geometric mean of 14 MPN/100 mL and a 90th

percentile of 43 MPN/100 mL) at several sites early in 2000. By late 2001, PS-2, off the mouth 

of Hat Slough (Figure 13), and many other sites were no longer approaching these criteria. The 

apparent trend was then recognized as part of a repeating seasonal pattern from fall storm-event 

loading. 

1

10

100

1000

Nov-98

Jan-99

Mar-99

May-99

Jul-99

Sep-99

Nov-99

Jan-00

Mar-00

May-00

Jul-00

Sep-00

Nov-00

Jan-01

Mar-01

May-01

Jul-01

Sep-01

Nov-01

Jan-02

Mar-02

May-02

Date

MPN/100 mL

FC data 30-sample geometric mean 30-sample 90th percentile

43 MPN/100 mL

14 MPN/100 mL

Figure 13. Fecal coliform sample results from site PS-2 of the Stillaguamish Tribe monitoring 

program in Port Susan. Commercial shellfish harvest criteria (14 MPN/100 mL geometric mean 

and 43 MPN/100 mL 90th percentile) used by the Washington State Department of Health are 

compared to the running 30-sample statistics. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 53

Table 12 shows the summary statistical data from all 16 Port Susan sites monitored by the 

Stillaguamish Tribe. Four sites met the 30-sample criteria in June 2002 (based on samples 

collected since September 2000). The sites were all located more than 5.6 km (3.5 mi) out from 

the mouth of Hat Slough (Figure 9): Kayak Point, Warm Beach Point, North Port Susan, and 

Peripheral Site #4 (PS-4). The statistics for sites PS-5 through PS-9 are based on fewer than ten 

samples, so they cannot be compared to the others. The South Branch Pilings site was very close 

to meeting the criteria, with a geometric mean of 12 MPN/100 mL and a 90th percentile of 

44 MPN/100 mL. It lies only 3.8 km (2.4 mi) away from Hat Slough. All other sites close to 

Hat Slough or near-shore discharge areas like Warm Beach Slough failed the criteria. 

Table 12. Fecal coliform statistics calculated for 30 consecutive samples collected by the Stillaguamish 

Tribe prior to June 27, 2002 at 16 sites in Port Susan and Hat Slough. Geometric 

mean and 90th percentile are in MPN/100 mL. 

Site Name 

Site Number

Hat 

Slough 

120 

West 

Branch 

121 

South 

Branch 

122 

South 

Branch 

Pilings 

123 

West 

Branch 

Point 

124 

Kayak 

Point 

125 

North 

Port 

Susan 

126 

West 

Branch 

Slough 

127 

Geometric 

Mean 

15 27 24 12 6.1 4.2 3.3 28 

90th percentile 64 98 102 44 31 20 12 100 

30-sample status 

(6/27/02) Fail Fail Fail Pass Pass Pass Fail 

Site Name 

Site Number

PS-2 

128 

PS-3 

129 

PS-4 

130 

PS-5 

137 

PS-6 

138 

PS-7 

139 

PS-8 

140 

PS-9 

148 

Geometric 

Mean 

21 14 5.7 21 19 32 15 3.9 

90th percentile 107 74 27 148 117 125 119 13 

30-sample status 

(6/27/02) Fail Fail Pass * * * * * 

* Insufficient data to determine status (n<10). 

The Stillaguamish Tribe did not increase their sampling frequency or focus on storm events 

during the 2000-2002 TMDL study period. This provides further evidence that changes in 

data sampling intensity were not the primary cause of the increased FC counts recorded 

throughout the basin. In fact, the data strongly suggest that seasonal factors and increased 

basin run-off influenced bacteriological quality in the bay. 

Correlation analysis was not successful in showing a consistent link between monthly or 

seasonal FC counts or loads from the Stillaguamish River (Hat Slough and South Pass) and their 

respective counts at the Port Susan sites. However, FC counts in the bay appeared to respond to 

loading from the river; i.e., river loads and the monthly bay-wide median FC counts followed 

similar rising and falling patterns (Figure 14). Most apparent are the peak loading months of 

June and November that correspond to bay-wide FC count increases in response to more frequent 

storm events. The surprise August 2001 storm event that became part of the database also 

influenced the average August FC load. 
Page 54 Stillaguamish Fecal and DO TMDL Submittal Report

0.0

5.0

10.0

15.0

20.0

25.0

30.0

35.0

40.0

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Month

Fecal Coliform (MPN/100 mL)

1.0E+10

1.0E+11

1.0E+12

1.0E+13

1.0E+14

Fecal coliform load (cfu/day)

Median FC Count Marine Criterion Stillaguamish River Load

14 MPN/100 mL

Figure 14. Monthly median fecal coliform (FC) counts from sites in Port Susan compared to 

estimated FC loads from the Stillaguamish River (Hat Slough and South Pass) for 1998 -2002. 

The FC loading months that affect water column FC counts in the bay appear to occur in the fall. 

Preliminary analyses showed that some failing sites in Table 12, such as PS-2 and PS-3, have 

seasonal FC counts (January - August) that produce geometric means and 90th percentiles within 

or nearly within the criteria. More data are necessary to confidently predict the seasonal 

FC loading effects on temporal FC counts in the bay. 

The FC contributions of small drainages and the Stillaguamish River were compared. Samples 

were collected by Ecology from 12 sites along the northeastern shore of Port Susan as 

Stillaguamish Tribe researchers were collecting samples in the bay. FC samples were collected 

monthly from February to November 2001 from South Pass, Juniper Beach, Hat Slough, and 

several small freshwater tributaries to Port Susan (Figure 9). These data are summarized in 

Table 13. Enterococci data also were collected and are summarized in Appendix D. 

Data at the 12 sites were highly variable, but a seasonal component was common in all data. 

Counts were lowest at all sites in February when all samples met FC criteria. On the other hand, 

counts were high at all sites during the August 2001 storm event when none met FC criteria. The 

two drains monitored from the Twin City Foods sprayfields had especially high counts in July 

and August. FC counts at the Warm Beach pump pond and three sites associated with it (Warm 

Beach Creek, Pasture drain, and Warm Beach WWTP outfall) gradually increased in April and 

stayed elevated through November. Lake Martha Creek had low counts until August, and then 
Stillaguamish Fecal and DO TMDL Submittal Report Page 55

had elevated counts the rest of the 2000-2002 study period. Counts from Unnamed Creek #0456 

south of Lake Martha Creek were sporadic after March, and the creek bed was dry in July and 

September. 

Table 13. Fecal coliform results from samples collected from freshwater and marine waters 

in and around northern Port Susan from February to November 2001. 

Fecal Coliform (cfu/100 mL) 

Sites to and in Port Susan 

Number 

of 

Samples 

Geometric 

Mean 

90th 

Percentile* 

Juniper Beach (Marine) 9 15 92 

South Pass (Marine) 10 29 125 

Twin City Foods Drain #1 9 513 3780 

Twin City Foods Drain #4** 9 149 1670 

Hat Slough at Marine Dr. 10 30 197 

Warm Beach Creek above outfall 10 46 457 

Warm Beach WWTP outfall 9 53 829 

Pasture Drain to Pump Pond 10 182 1000 

Pond or discharge to Slough 10 230 1130 

Lake Martha Creek at Soundview Dr. 10 82 694 

Unnamed Creek #0456 7 350 3640 

Class A Marine Water Criteria 14 43 

Class A Freshwater Criteria 100 200 

* The 90th percentile values are based on the FDA method assuming a lognormal distribution (Appendix B). 

** Drain #4 never discharged surface water to Hat Slough; the tide gate was always blocked with silt. 

Bold values do not meet criteria. 

The elevated bacteria counts in these small tributaries are potential sources of contamination to 

local recreational shellfish beds and to people enjoying beachside recreation, but their 

cumulative loading to Port Susan is minor compared to the Stillaguamish River. For example, 

the dike pond below Warm Beach Conference Center appears to influence Warm Beach Slough 

(site 127) results collected by the Stillaguamish Tribe (Table 12). The pond also discharges near 

other sources like Lake Martha Creek and Unnamed Creek. Together the three could pose a 

health risk at any time of the year because they are very accessible to people. Their influence on 

the FC counts at Warm Beach Point (site 124) and South Branch Pilings (site 123) farther out in 

Port Susan is less certain because these two sites were meeting or nearly meeting criteria 

(Table 12). 

Discharge volumes measured in all of the tributaries were usually less than 0.03 cms (1 cfs) 

during the surveys, so daily loads were a minute fraction of those from Hat Slough and South 

Pass. Some of the sites discharge only periodically through tide gates and by pumps, so their 

overall FC loading would be difficult to estimate. In one case, no surface water discharge to 

open water was observed; the tide gate between Hat Slough and Twin City Drain #4 was sealed 

with silt the entire study period. 

It appears that FC loads arriving from the Stillaguamish basin and small tributaries around the 

bay degrade bacteriological water quality. Some sources are active throughout the year, but 
Page 56 Stillaguamish Fecal and DO TMDL Submittal Report

Port Susan FC counts increase in June and again from September through December. This 

coincides with several possible sources of bacteria: 

• Rainstorms and increased discharge from the Stillaguamish River usually occur in the spring 

and fall. FC loads from the drainage basin are carried farther into the bay with larger 

freshwater volumes. 

• The river and surrounding areas may be carrying the ‘first flush’ of bacterial contaminants 

accumulated over the drier summer months. 

• Large flocks of snow geese, other waterfowl, and shorebirds arrive in September on 

migrations or to winter along the lower reaches of the river in and around Port Susan. Spring 

migration brings large flocks of shorebirds. 

• More severe winds arrive in the spring and autumn. Winds and wave action could resuspend contaminated sediment in the lower reaches of the river or estuary that was 

deposited earlier in the season. 

• Flooding is not uncommon during these months. Agricultural and residential lands lying in 

the flooded areas can contribute FC loads from freshly manured fields, inundated septic 

systems, and other sources. 

Synoptic and Storm-event Surveys 

The synoptic and storm-event surveys demonstrated that FC densities in the river responded to 

changes in surrounding land use and to storm runoff. Synoptic sampling conducted during an 

average flow event characterized the change in bacterial quality along the Stillaguamish River 

during a period of low surface runoff in the basin. Although the storm events were not 

monitored synoptically, they provide useful information about the response of FC in the river to 

periods of rainfall and high surface runoff. 

During the synoptic survey in September 2000, discharge in the river decreased over the three 

days. The estimated mean daily flow at the Interstate 5 (I-5) site dropped from 59.5 cms (2100 

cfs) to 28.6 cms (1010 cfs). FC sample results in the mainstem on all three days were 100 

cfu/100 mL or less, and samples taken from sites up both forks were below 40 cfu/100 mL. 

Portage Creek and Arlington WWTP had FC counts greater than 100 cfu/100 mL. The FC 

counts decreased at most mainstem sites over the three days. The estimated FC load at the I-5 

site decreased by 75% between the first and third day. 

After considering natural FC sample variability and a range of die-off rates, FC count increased 

in reaches that could not be attributed to tributary inputs. Significant and fairly consistent 

chloride and nutrient increases also occurred in reaches between Arlington and Armstrong Creek 

(km 27.7 to 24.7), on the North and South Branch below I-5, and between Silvana and Marine 

Drive (km 9.7 to 4.2) during the three days. Unidentified sources (e.g., unmonitored tributaries, 

drains, or nonpoint sources) along these reaches of the mainstem were suspected. The 

unidentified sources were simulated using the QUAL2Kw model by adding sources with a 

loading equivalent to one-third to four times the size of Portage Creek’s FC load. The actual 
Stillaguamish Fecal and DO TMDL Submittal Report Page 57

volume of these sources and their bacteria counts are not known. However, the simulation 

results with the sources in place fit field data better than without them (Figure 15). \

0

10

20

30

40

50

60

-5 0 5 10 15 20 25 30

Distance downstream (Km)

Fecal coliform (cfu/100mL)

Bact-data

95% CI

With NPS

Without NPS

Confluence of forks Hatt Slough Portage Creek

NPS NPS

Figure 15. QUAL2Kw simulation results compared to fecal coliform data (with 95% confidence 

interval) collected from the lower Stillaguamish River on September 13, 2000. Unidentified 

source loads (NPS) at 4 km and 21 km were added to calibrate model 

with field data. 

The survey under these conditions demonstrated that active sources of FC are present in the 

basin under average-flow conditions when transport from surface run-off is low. The FC loads 

from other unidentified sources may be present and increase the instream fecal counts. 

According to the model simulation results for the September 13th example, the unidentified 

sources increased FC loads at Hat Slough by at about one third. The additional load degrades the 

water quality in the river and in Port Susan even though the FC counts were well within criteria. 

FC results from the two, 2-day storm-event monitoring surveys demonstrated that areas of the 

Stillaguamish River basin still have significant sources of bacteria that cause water quality 

criteria violations and require controls. During each storm event, a third or more of the 42 

samples collected from the mainstem, forks, tributaries, and point source sites had FC counts 

greater than 200 cfu/100 mL. Tributaries in the lower basin had the highest FC counts, and FC 

counts generally increased in the mainstem and forks from the upper basin to the mouth. Results 

from a representative set of sites are shown in Table 14. 
Page 58 Stillaguamish Fecal and DO TMDL Submittal Report

Table 14. Fecal coliform results at selected sites in the Stillaguamish River basin for samples 

collected during two, 2-day storm-event surveys in 2001. 

June 12 June 13 November 14 November 15 Site 

(cfu/100 mL) (cfu/100 mL) 

South Fork below Granite Falls 92 17 28 22 

Jim Creek at Jordan Road 320 150 160 20 

South Fork at Twin Rivers 310 31 92 26 

North Fork at C-Post Bridge 67 4 37 17 

North Fork at Twin Rivers 240 43 Not accessible 40 

Arlington WWTP 36 26 80 440 

Stillaguamish River below Arlington 540 38 330 37 

Armstrong Creek below Hatchery 2,800 75 200 170 

March Creek 18,000 3,300 550 900 

Stillaguamish River at Interstate 5 520 100 380 34 

Portage Creek at 212th 6,300 770 350 1,600 

Pilchuck Creek at Jackson Gulch 950 75 140 43 

Stillaguamish River below Silvana 360 160 190 60 

Glade Bekken at Terrace Road 52,000 2,500 360 310 

Stillaguamish River at Hat Slough 680 130 380 110 

As might have been expected, the FC counts from the forested and less developed upper basin 

forks were much lower than from the more developed lower mainstem. Since the two forks 

comprise approximately 80% of the watershed area and deliver about 80% of the annual 

discharge, the bacterial quality of the water from the upper basin has a large influence on the 

lower mainstem. As observed in the historical data by Thornburgh and Williams (2001), FC 

counts in the lower basin generally increase downstream from Arlington to Hat Slough. 

Samples collected at sites located near the confluence of the forks (S. Fork at Twin Rivers and N. 

Fork at Twin Rivers) had higher FC counts than upstream sites (Table 14). FC counts at both 

Twin Rivers sites were greater than 200 cfu/100 mL on the first day of the June storm survey. 

FC counts at the sites in the upper reaches of the South Fork and North Fork were usually two to 

ten times less than counts at the Twin Rivers confluence. This increase in FC bacteria may be 

related to the increased development along the lower reaches of the forks, and up more 

developed tributaries like Jim Creek. 

The samples collected on the first day of both storm events from nearly all of the mainstem sites 

downstream of the forks were greater than 200 cfu/100 mL. Most June FC counts were greater 

than 500 cfu/100 mL, and most November FC counts were greater than 300 cfu/100 mL (Table 

14). The bacterial response in the two forks and the mainstem to these two storm events was of 

short duration; i.e., the FC counts returned to much lower levels on the second day of monitoring 

immediately after the peak flows had passed. 

At least one FC sample collected from each of the six lower valley tributary sites and from the 

Arlington WWTP effluent had a count greater than 200 cfu/100 mL during the storm events 

(Table 14). All samples collected during the storm events from March Creek, Portage Creek, 

and Glade Bekken were greater than 200 cfu/100 mL. FC counts greater than 1000 cfu/100 mL 
Stillaguamish Fecal and DO TMDL Submittal Report Page 59

were reported in samples from these three creeks, Armstrong Creek, and Kackman Creek. All 

five tributaries have reaches with potential residential, agricultural, and roadway stormwater 

sources of FC. 

In contrast to the mainstem FC pattern, most tributary FC counts appeared to stay elevated for 

longer, or they experienced a lag in the peak FC count. For example, March Creek, Portage 

Creek, Kackman Creek, and Arlington WWTP had higher FC counts the second day of the 

November event, while mainstem FC counts had peaked the first day (Table 14). Pilchuck 

Creek, the largest tributary sub-basin in the lower basin, had a FC pattern similar to the mainstem 

and forks. Runoff from the large undeveloped areas in the Pilchuck and upper basin of the 

Stillaguamish River may provide water with low bacterial counts that can dilute the FC loads 

from more developed reaches and tributaries. 

 

The effect of the FC loads from tributaries, point sources, and suspected nonpoint sources on the 

Stillaguamish River was difficult to assess. Sampling rapidly changing hydrographs in a large 

basin with several tributaries and few available staff resources prevented a synoptic monitoring 

approach during the storms. Estimates based on the few samples collected indicated that Portage 

Creek and Pilchuck Creek delivered the largest FC tributary loads to the lower basin. FC loading 

from the Arlington WWTP was minor compared to the tributary loads because the WWTP 

discharge volumes were much lower than the tributary volumes. FC loads from other nonpoint 

sources along the lower mainstem were suspected, but they could not be estimated because of 

variability in the mainstem. 

Although the FC counts were much lower in November than in June, the estimated FC loads 

from the mainstem Stillaguamish River to Port Susan were much higher. During the June storm 

event, the Stillaguamish River at Interstate 5 (I-5) had an estimated mean daily flow of 7250 cfs. 

The FC count at I-5 was 520 cfu/100 mL, and at Hat Slough it was 680 cfu/100 mL. During the 

November storm, the estimated flow at I-5 was 19,000 cfs. The FC counts at I-5 and at Hat 

Slough were 380 cfu/100 mL A rough estimate would be that the November storm delivered 

about twice the FC load to Port Susan as the June storm on the first day. On the second day of 

the June storm, the FC load was about 13% of the first day’s load to Port Susan. A similar 

estimate was made for the November storm where the FC load on the second day dropped to 

about 15% of the first day’s load. 

Freshwater Recreation Area Sampling 

Ecology sampled for FC weekly for a five-week period in August and September 2000 at seven 

informal recreational bathing beaches. These data were presented earlier by Joy (2001), but are 

repeated here to demonstrate FC variability within a season and potential recreational use 

impacts. A statistical summary of the results of the TMDL freshwater beach survey is shown in 

Table 15. 
Page 60 Stillaguamish Fecal and DO TMDL Submittal Report

Table 15. Statistical summary of fecal coliform samples (n=5) collected weekly from 

seven informal recreational beach sites in the Stillaguamish River basin from August 7 to 

September 5, 2000. 

Fecal Coliform (cfu/100 mL) Informal Recreational Beach Sites Geometric Mean 90th percentile* Range 

S.F. Stillaguamish at Jordan 34 63 18 – 55 

S.F. Stillaguamish at Twin Rivers 34 112 10 – 130 

N.F. Stillaguamish at Twin Rivers 19 49 9 – 61 

N.F. Stillaguamish at Whitman Br. 3 11 1 – 10 

Stillaguamish River at Marine Dr. 27 74 9 – 74 

Pilchuck Creek at Jackson Gulch 86 285 40 – 280 

Church Creek at Stanwood Park 101 197 57 - 190 

Current State Class A Criteria 100 200 

* The 90th percentile values are based on the FDA method assuming a lognormal distribution (Appendix B). 

Bold values do not meet current Washington State FC criteria. 

Church Creek at Stanwood Park did not meet the geometric mean FC criterion, and the 90th

percentile statistic was just under the 200 cfu/100 mL criterion. The Pilchuck Creek site FC 

densities did not meet the 90th percentile criterion. The other five sites met both parts of the FC 

criteria. 

 

Church Creek appeared to be the most popular area, but not by swimmers. Children were often 

seen playing near or in the creek. Pilchuck Creek and the Twin Rivers Park beaches (the 

confluence of the North and South forks of the Stillaguamish River) were more likely to have 

swimmers. According to these data, Pilchuck Creek swimmers and children playing in Church 

Creek would probably be at a slightly greater health risk. 

Critical Conditions and Loads 

The analyses of the FC distributions show that the critical season for meeting Class A criteria in 

the major forks, lower mainstem, and most tributary sites occurs from May through November. 

However, FC loads and counts are most likely to become elevated during storm events 

throughout the year. Although primary contact recreation is not popular during storm events or 

during all of this critical period, Washington State FC criteria apply to primary and secondary 

recreation uses. Exposure to waterborne bacteria during secondary recreational uses can occur at 

any time of the year. 

June and October through January appear to be the critical months for FC loading to Port Susan, 

resulting in fewer sites in the bay in compliance with DOH or Class A marine criteria 

(Figure 14). However, storm events can increase FC loading to Port Susan throughout the year. 

The available data support or suggest the following reasons for the critical season in fall: 

 Median FC loads at the Stillaguamish River at I-5 increase from 3.2 x 1011 cfu/day in 

September to 4.5 x 1012 cfu/day October, and then often remain elevated through the next 

few months (Figure 16). 

 A few more Port Susan monitoring sites meet Class A criteria, if only January - August data 

are used. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 61

 The increasing frequency and intensity of storm events in the fall can dislodge and carry 

bacterial contaminants accumulated over the drier summer months. 

 Large flocks of snow geese, shorebirds, and waterfowl stop or winter along the lower reaches 

of the river and in the estuary beginning in September. These birds could be the source of a 

significant seasonal FC load (Table 16). 

 More severe winds arrive in the autumn. Winds and wave action re-suspend bacteriacontaminated sediment in the lower reaches of the river or estuary that was deposited earlier 

in the season. Scouring action by increased river and tributary flows could also re-suspend 

contaminated sediments previously delivered from upland areas. 

 Flooding is not uncommon during these months. Agricultural and residential lands lying in 

the flooded areas can contribute FC loads from manured fields, septic systems, and other 

sources. FC Load 

MONTH 

 10000

100000

 1000000

10000000

 100000000

1000000000

JAN FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC 

1994-2002 

K-W 50% 

(8) 

(8) 

(8) 

(8) 

(8) 

(8) 

(8) 

(7) 

(7) 

(8) 

(7) 

(8) 

Figure 16. A box-plot summarizing monthly fecal coliform loads (cfu/day x 106) from data 

collected by Ecology at the Stillaguamish River at Interstate 5, #05A070, from 1994 to 2002. The 

box-plot depicts the median, 10th, 25th, 75th, and 90th percentiles, and the range. 
Page 62 Stillaguamish Fecal and DO TMDL Submittal Report

Table 16. Bird population data for northeast Port Susan, Livingston Bay, and the Stillaguamish River 

delta (Cullinan, 2001), and estimates of the daily fecal coliform load. 

Bird Season Sighted Average 

Population

Estimated 

FC Production 

(cfu/day) x 1012

Maximum 

Population 

Estimated 

FC Production 

(cfu/day) x 

1012

Trumpeter 

Swan 

Winter 51 0.02 139 0.06 

Snow Goose Winter 9,700 3.9 25,000 10 

Ducks Winter 4,040 6.9 6,864 11.7 

Shorebirds Fall Migration - - 50,000 40 

Shorebirds Winter 24,175 20 31,050 25 

Shorebirds Spring Migration 34,350 25 50,000 40 

The estimated average seasonal FC loads contributed from the Stillaguamish River (Hat Slough 

and South Pass) to Port Susan during the 2000-2002 TMDL study period varied between 3.8 x 

1012 cfu/day for July through September, and 1.4 x 1013 cfu/day for October through December. 

The November storm event discharged an average of 1.1 x 1014 cfu/day over two days, 

demonstrating the importance of FC loading from short-term events. 

In Table 16, estimates of potential daily FC loads to Port Susan from wildfowl were calculated 

based on literature values for FC concentrations in fecal material and daily manure production 

from domestic ducks, geese, and chickens (ASAE, 1998). The daily or seasonal FC loadings 

from the various wildfowl to Port Susan depend on their accustomed habitat relative to water. 

For example, the geese and swans spend much of the time on fields and nearshore wetlands, so 

much of their FC loading would be through land delivery and runoff through drains and creeks. 

The shorebirds are more likely to spend more time on the tideflats, so FC loading would be a 

function of exposure of the feeding areas on tideflats and then tidal inundation. Ducks are 

probably the most pelagic of the species listed. Their FC loading would tend to be directly to the 

water column, although they might seek more protected sloughs during rougher weather. 

The contribution of seal fecal material to FC concentrations in the water column is not well 

documented. The contribution seals make to FC loads in Puget Sound harbors and bays can vary 

greatly (Calambokidis, McLaughlin, and Steiger, 1989). Bacterial densities in seal fecal material 

(1.7 to 55 x 109

 cfu/day), dispersion of fecal wastes near haul-out areas, and flushing efficiency 

of the embayment can affect the FC loading from seals. If a seal produces 2.8 x 1010 cfu/day 

(average of the range quoted above), then 300 seals in Port Susan have the potential for 

contributing a daily fecal load of approximately 8.5 x 1012 cfu/day to the bay. 

The loading from wildlife can be significant. If the average daily winter FC loading from seals 

and waterfowl were directly discharged to Port Susan, it would be more than the estimated daily 

average winter FC loading from the Stillaguamish River. Fortunately, only a fraction of the 

wildlife FC load is directly available to water since the wildlife are not in the water all of the 

time. Their seasonal impact on FC loading can still have an effect on areas of the bay. In an 
Stillaguamish Fecal and DO TMDL Submittal Report Page 63

example from Massachusetts, researchers calculated that 67 percent of the annual FC load in 

Buttermilk Bay was from waterfowl; the loading was seasonal (December through March), but it 

was dispersed throughout the bay rather than concentrated in a single area (Weiskel, Howes, and 

Heufelder, 1996). 

The increases in FC loading in the fall season from the Stillaguamish River and from wildlife are 

also accompanied by internal Port Susan sources. Estuarine mud often has higher counts of 

bacteria and viruses than overlying water (Thomann and Mueller, 1987). Many researchers also 

have found that bacteria and viruses survive for longer periods in the mud than in open water. 

There is also evidence that lower salinities can also release bacteria that are adsorbed to sediment 

(Erkenbrecher, 1981). Rougher weather and higher river flows in fall can re-suspend 

contaminated sediments deposited at the mouth of the estuary during earlier periods. The lower 

salinities caused by increased freshwater input can also release more bacteria from the sediment 

into the water column. Estimating the FC loading from these sources would be difficult. The 

phenomenon is another potential source of loading to consider when assessing the water quality 

of Port Susan. Since re-suspension is a possible source of FC loading in Port Susan, the loading 

from surrounding rivers and streams throughout the year is important to consider. 

Summary of Fecal Coliform Results 

FC counts at most sites monitored under more than one agency (Ecology, Stillaguamish Tribes, 

Snohomish County, and Water and Wastewater Services at Warm Beach) operating from June 

2000 to June 2001 were combined to get a comprehensive picture for the 2000-2002 TMDL 

study period. The geometric mean and 90th percentile statistics calculated for FC at most lower 

basin mainstem and tributary sites did not meet the state FC criteria (Table 17). The final 

determination of criteria compliance will be made after an analysis of critical conditions for each 

site in the Loading Capacity section of this report. 

According to the data collected during the TMDL study period, all sites located along the upper 

forks met Class A freshwater criteria, as did Hat Slough at the Boat Launch. Mainstem sites 

located below Arlington, at I-5, and Hat Slough at Marine Drive did not meet the 90th percentile 

criterion. Although some improvements were seen in several smaller tributaries, only samples 

from Jim Creek met both parts of the state criteria. Some of the creeks appear to have chronic 

FC sources. For example, data from Church Creek/Jorgenson Slough, Irvine Slough, Miller 

Creek, Portage Creek, Fish Creek, Glade Bekken, Kackman Creek, and Harvey Creek met 

neither the geometric mean nor the 90th percentile criteria. Data at other sites met the geometric 

mean criterion, but had episodic events with elevated FC counts more than 10 percent of the 

time, failing the second part of the state FC criteria. 

The two Hat Slough sites are only 230 meters apart, but the statistical results in Table 17 are 

quite different. The differences create some difficulties in characterizing the bacteriological 

quality of the reach. Several factors may contribute to the differences, including (1) two 

methods of analysis were used; the samples collected downstream at the Boat Launch were 

analyzed by MPN, and the upstream Marine Drive samples were analyzed by MF (see 

Applicable Water Quality Criteria for definitions of MPN and MF); (2) samples were collected 

at different times; and (3) the area is tidally influenced. The last factor may have caused a 
Page 64 Stillaguamish Fecal and DO TMDL Submittal Report

difference because the samples at the Boat Launch were usually taken at high ebb tide, and the 

samples upstream at Marine Drive were not. 

Table 17. Statistical summaries of fecal coliform samples collected from sites in the Stillaguamish 

River basin during this TMDL daily load study (June 2000 to June 2002). Geometric mean and 90th 

percentile are in colony forming units/ 100 milliliters. 

Site Number of 

samples 

Geometric 

mean 

90th

percentile 

Douglas Slough 42 44 808 

Irvine Slough 13 680 16,205 

Jorgenson Slough 27 295 1,863 

Church Creek at Park 27 104 435 

Miller Creek 17 326 1,715 

Warm Beach Creek above WWTP 19 70 578 

Agricultural Drain to Warm Beach 19 121 572 

Warm Beach Dike Pond 19 189 1025 

Lake Martha Creek 51 92 1,008 

Hat Slough at Marine Drive 56 41 261 

Hat Slough at Boat Launch 41 17 63 

Glade Bekken 27 171 1,558 

Pilchuck Creek 40 46 312 

Portage Creek at 212th 32 236 2,032 

Portage Creek at 43rd 19 149 722 

Fish Creek 21 206 4310 

Stillaguamish R. at Interstate 5 33 26 223 

March Creek 7 475 8,760 

Armstrong Creek at Mouth 4 46 209 

Kackman Creek 10 165 669 

Armstrong Creek at Hatchery 12 86 667 

Harvey Creek at Grandview Road 6 317 1527 

Stillaguamish R. below Arlington 12 48 412 

Stillaguamish R. above Arlington 20 36 181 

S.F. Stillaguamish at Arlington 35 27 156 

Jim Creek at Mouth 12 55 190 

Jim Creek at Whites Road 6 17 52 

S.F. Stillaguamish at Granite Falls 30 6 40 

N.F. Stillaguamish at Twin Rivers 9 33 116 

N.F. Stillaguamish at Cicero 30 13 82 

N.F. Stillaguamish at Whitman Br. 17 11 54 

N.F. Stillaguamish at C-Post Br. 12 9 37 

N.F. Stillaguamish at Darrington 25 8 47 

* Bold values do not meet the fecal coliform criteria (Table 6) 
Stillaguamish Fecal and DO TMDL Submittal Report Page 65

Some of the summary statistics verify findings made during other TMDL tasks. For example, 

the synoptic survey indicated FC counts increased downstream in both forks, and also in some 

reaches from the confluence of the forks to Port Susan. Also, storm-event data demonstrated that 

runoff can seriously increase FC counts in waters throughout the basin, but the smaller tributaries 

are affected most severely. Finally, some sites like Pilchuck Creek occasionally experience 

FC counts above 200 cfu/100 mL during the summer recreational season, as well as during storm 

events throughout the year. 

Port Susan water quality will depend on the freshwater sites coming into more consistent 

compliance with FC criteria. The Port Susan sites farther away from the mouth of Hat Slough 

and South Pass were more likely to meet marine water criteria. The increased FC loading from 

the Stillaguamish basin during seasonal storm events, especially in the fall, have an effect on 

Port Susan FC counts. Additional FC loading from small tributaries around the bay, internal resuspension of bacteria-contaminated sediment, a resident seal population, and the arrival of large 

numbers of migratory waterfowl may increase bacteria counts in Port Susan. 

The following conclusions and additional observations were reached from evaluating the FC 

density data collected in 2000 and 2002 relative to past data. 

• The FC bacteria data sets for the upper South Fork, upper North Fork, and Hat Slough at the 

boat launch meet freshwater Class A criteria (Table 17). 

• More than 10 percent of the FC counts at sites just below the confluence of the forks, below 

Arlington, and at I-5 are greater than 200 cfu/100 mL. It is unlikely that Arlington WWTP 

effluent is a primary source of elevated FC in this area since its FC load is small. Data 

collected from sites above the outfall indicate a FC problem during storm runoff events. 

• FC count reductions along the mainstem and in the two forks occurred after 1995 and 1996. 

Decreasing trends at many sites were interrupted by increased FC counts reported in 2001. 

This may suggest that improvements since 1996 have not consistently reduced FC counts in 

those areas. 

• The elevated FC counts in Port Susan are usually associated with short pulse storm events 

during the spring and through the fall. The fall storms and increased discharge to Port 

Susan prevent many of the sites in the bay from complying with Class A marine water 

criteria. 

• Only one of the tributaries evaluated in the basin met both parts of the state Class A 

FC criteria: Jim Creek. Only six sites on other tributaries had geometric mean counts 

below 100 cfu/100 mL: Pilchuck Creek at Jackson Gulch Road, the mouth of Armstrong 

Creek and below the hatchery, Lake Martha Creek, Warm Beach Creek, and Douglas 

Slough. 

• Glade Bekken experienced a significant improvement in FC counts in 1999 to 2001 

compared to 1996 to 1998. This may be a result of Snohomish Conservation District and 

Snohomish County Surface Water Management efforts upstream of Silvana Terrace Road. 

• FC counts collected at Portage Creek at 212th, the last crossing before the confluence with 

the Stillaguamish River, appear to have increased significantly in 2001 and 2002. No trend 

was observed in the data from Portage Creek upstream at 43rd. A major tributary, Fish 

Creek, showed significant improvement in FC counts from 1997 to 2002 compared to 
Page 66 Stillaguamish Fecal and DO TMDL Submittal Report

1994 to 1996. This suggests that a FC source is located between 212th and these upstream 

monitoring sites. 

• FC counts in March Creek appear to increase greatly during storm events, but the data set is 

too small to totally characterize an annual pattern. 

• Although geometric mean FC counts at the mouth of Armstrong Creek and below the 

hatchery met the Class A criteria, the counts upstream in Kackman Creek and Harvey Creek 

did not meet any part of the criteria. 

• Unidentified sources may be increasing FC counts in the mainstem: between Arlington and 

Armstrong Creek, on the North Branch below I-5, and between Silvana and Marine Drive. 

• Port Susan FC counts were decreasing in 1999, but they increased at many sites in 2000 to 

2002. FC loads arriving from the Stillaguamish basin and small tributaries around the bay 

in September through December appear to degrade bacteriological water quality. 

• Intermittent discharges from pump systems (Irvine Slough and Warm Beach Dike Pond) 

and drains with tide gates could be significant sources of local FC loading in the lower 

Stillaguamish River and in localized areas like Warm Beach Slough. 

Dissolved Oxygen 

Current Conditions and Trends 

Most dissolved oxygen (DO) data collected in the Stillaguamish River basin have been from 

instantaneous daytime ‘grab’ measurements. The 303(d) listings for low DO were based on 

instantaneous measurements made in Pilchuck Creek and Portage Creek (both Class A), the 

South Fork above Granite Falls (Class AA), and the mainstem Stillaguamish River below 

Silvana and in Hat Slough (Class A). The listings were based on samples collected in 

1994-1996. 

A diel study conducted below the Arlington WWTP by Earth Tech (1997) consultants found that 

DO concentrations at RKM 21.7 (RM 13.5) upstream of the Interstate 5 bridge dropped to 

7.2 mg/L in the early morning, and rose to 11 mg/L in the late afternoon in August 1997. The 

consultants modeled the effluent biochemical oxygen demand (BOD) from the Arlington 

WWTP. The model demonstrated that effluent BOD and nitrogenous oxygen demand1

 had little 

effect on instream DO concentrations. They considered oxygen demand from periphyton 

biomass respiration the primary cause of low diel DO concentrations during a survey. Data from 

this study were not included in the 1998 303(d) database, so the reach was not listed. 

Ecology, Snohomish County, and the Stillaguamish Tribe collected a combination of 

instantaneous and diel DO measurements in the basin during the 2000-2002 TMDL study period. 

Results from instantaneous measurements taken at 36 sites in the basin are summarized in 

Table 18. The sites were located along the North and South forks, the mainstem Stillaguamish 

River, several tributaries to the mainstem, and small drainages to Port Susan south of Hat 

Slough. 

 

1

 Nitrogenous oxygen demand is a term used to describe the biochemical oxidation of ammonia to nitrite and nitrate. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 67

Table 18. A summary of dissolved oxygen concentrations from grab samples collected in the 

Stillaguamish River basin by Ecology, Snohomish County, and the Stillaguamish Tribe from 

June 2000 to June 2002. 

Site Number 

of Samples 

Concentration 

Range (mg/L) 

10th Percentile 

concentration 

Twin City Foods Drain #4 (silted shut) 8 1.2 – 18.8 3.3 

Warm Beach Creek above WWTP outfall 7 3.8 – 8.4 3.9 

Pasture Drain to Pump Pond 6 4.1 – 12.0 4.7 

Pond or discharge to Warm Beach Slough 7 3.0 – 9.1 3.8 

Lake Martha Creek 10 8.8 – 12.1 9.4 

Unnamed Creek #0456 7 8.6 – 11.8 8.7 

Hat Slough at Marine Drive 49 8.0 – 13.2 9.0 

Stillaguamish River at Old Channel split 2 5.7, 10.1 - 

Glade Bekken at Silvana Terrace Road 33 7.5 – 14.0* 9.5 

Stillaguamish River below Silvana 7 9.8 – 13.2 9.9 

Stillaguamish River (Cook or South Slough) 11 10.2 – 12.8 10.4 

Stillaguamish River (North Channel) at Silvana 7 9.4 – 12.9 9.6 

Pilchuck Creek at Jackson Gulch Road 37 7.6 – 13.6 8.5 

Portage Creek at 212th 32 5.1 – 12.2 5.5 

Portage Creek at 15th 10 3.7 – 7.2 4.2 

Portage Creek at 43rd 25 6.4 – 11.4 6.8 

Krueger Creek at Burns Road 5 8.4 – 11.6 9.5 

Portage Creek at Highway 9 10 8.8 – 11.6 9.3 

Prairie Creek at 69th and 204th 9 9.7 – 14.2 10.4

Fish Creek 24 9.2 – 14.0 9.8 

Stillaguamish River at Interstate 5 37 9.1 – 14.4 9.7 

March Creek at 220th NE 6 4.8 – 8.0 4.8 

Armstrong Creek at Mouth 3 9.5 – 10.3 9.7 

Kackman Creek at 252nd 6 6.6 – 9.0 7.0 

Armstrong Creek at Hatchery 6 9.3 – 11.6 9.5 

Harvey Creek at Grandview Road 9 9.8 – 11.8 10.0 

Stillaguamish River above Arlington 32 8.9 – 13.4 9.9 

S.F. Stillaguamish at Arlington 38 9.5 – 14.6 9.9 

Jim Creek at Mouth 4 10.4 – 12.5 10.7 

S.F. Stillaguamish at Jordan Walkway 9 10.0 – 12.5 10.1 

S.F. Stillaguamish at Granite Falls (Class AA) 28 10.0 – 14.3 10.7 

N.F. Stillaguamish at Twin Rivers 10 9.8 – 11.6 10.3 

N.F. Stillaguamish at Cicero 32 10.1 – 14.3 10.8 

N.F. Stillaguamish at Whitman bridge 9 10.8 – 11.6 11.0 

N.F. Stillaguamish at C-Post bridge 4 10.7 – 13.0 10.8 

N.F. Stillaguamish at Darrington 25 10.8 – 14.0 11.2 

Bold values do not meet the dissolved oxygen criteria. 

* Glade Bekken had only a single violation of the criteria, so it does not meet the 303(d) listing policy (see text). 
Page 68 Stillaguamish Fecal and DO TMDL Submittal Report

The data summarized in Table 18 do not include all of the data collected during the 2000-2002 

TMDL study period. DO data from the Old Stillaguamish Channel and its tributaries will be 

discussed in a future report. Several mainstem sites were only monitored a few times. Data at 

these sites were not summarized because they were all well within the DO criterion, and they are 

available in the Data Summary Report (Coffler, Gridley, and Joy, 2004). Data obtained from 

continuously recording DO probes will be discussed later in this report (Dissolved Oxygen in the 

Stillaguamish River below Arlington).

Based on the combined data, 11 sites did not meet the Class A criterion of 8 mg/L (Table 18). 

The lowest DO concentrations at all sites were reported from measurements made during the 

months of May through October. Applying a 0.5 mg/L safety factor to the 10th percentile 

concentration to account for diel, minimum DO concentrations did not identify any additional 

sites (see Analytical Framework for explanation). All but one of the sites are located on 

tributaries or drains to the lower Stillaguamish River or to Port Susan. 

• Twin City Foods Drain #4 

• Warm Beach Creek above the Warm Beach WWTP outfall 

• Pasture Drain and Pond (2 sites) to Warm Beach Slough 

• Pilchuck Creek 

• Portage Creek (3 sites) 

• March Creek 

• Kackman Creek 

• Stillaguamish River at the Old Channel Split 

All appear to have fecal coliform contamination problems as well, according to the statistical 

summaries in Table 17. 

Past monitoring data have been used to place the lower Stillaguamish River on the 1998 303(d) 

list. During low-flow periods, the lower Stillaguamish River from around RKM 4.8 (RM 3) to 

Hat Slough can experience short-term depressed DO concentrations. Some of the reaches below 

the Marine Drive bridge may be influenced by low-DO marine water from Port Susan (Klopfer, 

2000). Upstream of the bridge, the unusually low DO concentrations at midday are caused by 

deoxygenated water from the Old Stillaguamish Channel flowing back into the main river 

channel. This was observed during the September 13, 2000 synoptic survey (Coffler, Gridley, 

and Joy, 2004). The DO concentration near the bifurcation point of the two channels (Site 

#05TMS3) was 5.72 mg/L. DO concentrations in the Old Stillaguamish Channel have been as 

low as 2.6 mg/L at the Norman Road bridge (Site #05TOC4), and five-day BOD concentrations 

of 3 - 5 mg/L were recorded (Coffler, Gridley, and Joy, 2004). 

The Stillaguamish River reach affected is limited to the right side of the main channel and is 

dependent on the following factors: 

• The tidal volume and tidal stage timing differences in the Old Channel and Hat Slough. 

• The oxygen depletion in the upper reaches of the Old Stillaguamish Channel. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 69

• The direction, dilution, and dispersion characteristics of the Stillaguamish River. 

In late 2002, a tide gate was installed in the Old Stillaguamish Channel to operate during the 

low–flow season starting in 2003 (SIRC, 2002). The gate is designed so that water is allowed to 

pass from the Stillaguamish River to the Old Stillaguamish Channel, but not in the reverse 

direction. If the tide gate works as designed, low DO water will not reach the mainstem and Hat 

Slough from the Old Channel. The low DO concentration problem in the Old Stillaguamish 

Channel and the effectiveness of the tide gate will be addressed in a future report. 

Glade Bekken had a single DO measurement below 8 mg/L in May 2001, but the 10th percentile 

value of the data set was well above the 8.5 mg/L concentration of concern. Past studies by 

Snohomish County have not found DO violations along the mainstem of the creek (Thornburgh, 

2001). The 303(d) listing policy for Ecology requires violations from instantaneous data to 

occur at least three times (Ecology, 2002). Therefore, Glade Bekken should be monitored more 

intensively in the future, but should not be considered for a load capacity analysis at this time. 

Pilchuck Creek was on the 1998 303(d) list for DO based on data collected by Snohomish 

County prior to 1995. Pilchuck Creek had three excursions below 8 mg/L within the current 

monitoring period (2000 – 2002), the first since 1994 – 1995 when it was listed. Two excursions 

below the criterion in Pilchuck Creek were on consecutive days in August 2000 (7.89 and 

7.9 mg/L), and the third was in May 2001 (7.56 mg/L). The August values were at 80% 

saturation. The May concentration was at 69% saturation. The rank 10th percentile DO 

concentration for Pilchuck Creek is 8.5 mg/L based on instantaneous samples collected by 

Snohomish County and Ecology, just at the concentration recommended to account for diel 

minima within the DO criterion. No other water quality parameters were out of compliance with 

criteria during the three events that would help to identify the source(s) of the low DO 

concentrations. 

Pilchuck Creek data, collected since 1994, showed an improving DO trend in Pilchuck Creek 

until it was interrupted in 2000. Temperature data continue to show a significant cooling trend. 

Temperature is often a controlling factor for DO concentrations because lower water 

temperatures will increase DO solubility. In some cases, lower temperatures can also indicate 

the influence of local groundwater infiltration. 

The Pilchuck monitoring site at Jackson Gulch bridge is located in a floodplain, near the 

confluence with the Stillaguamish River, and downstream of Interstate 5. During the low-flow 

season, the monitoring site on Pilchuck Creek is a large, slow pool. The pool could be a source 

of sediment oxygen demand or heterotrophic bacteria activity in a hyporheic exchange zone 

(see Dissolved Oxygen in the Stillaguamish River below Arlington). The oxygen demand could 

be from a mix of autochthonous (generated within the stream) and allochthonous (delivered to 

the stream) materials. Wetland areas and ground water could also contribute water with 

naturally low oxygen concentrations. 

Oxygen-demanding wastes could come from upstream from anthropogenic and natural sources. 

Reaches immediately upstream of the sampling site drain forested lands, with scatterings of 

wetlands, agriculture, and residential areas. All of these land uses have sources of organic 

material that can be delivered to the creek and can contribute to oxygen demand. Manure from 
Page 70 Stillaguamish Fecal and DO TMDL Submittal Report

livestock operations has historically been a source of excessive oxygen-demanding pollutants in 

the basin. The four dairies listed in 1996 in the Pilchuck Creek sub-basin are no longer active, 

but there are non-commercial farms and equestrian centers in the lower watershed (Thornburgh 

and Williams, 2001). A Washington State Department of Transportation (WSDOT) map shows 

several stormwater outfalls to Pilchuck Creek from Interstate 5 and the Jackson Gulch 

interchange upstream of the sampling site. Storm water from several arterial county roads, 

including Jackson Gulch Road, also enter the creek or its tributaries. 

Two reaches of Portage Creek were on the 1998 303(d) list (Table 1). Portage Creek has a long 

history of low DO concentrations in its lower reaches during the daylight hours. The low DO 

concentration can occur from May through November (Figure 17). Data collected at sites from 

1989 to 1995 in these lower reaches caused the 1998 303(d) listings. mg/L

MONTH 

 4

 5

 6

 7

 8

 9

10

11

12

13

JAN FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC 

1997-2002 

K-W 99% 

WQ Standard 

(5) 

(4) 

(5) 

(4) 

(4) 

(4) 

(4) 

(4) 

(4) 

(5) 

(5) 

(5) 

Figure 17. A box-plot of monthly dissolved oxygen measurements collected at Portage Creek at 

212th NE by the Snohomish County Surface Water Management Program from October 1997 to 

April 2002. The monthly range of measurements is compared to the 8 mg/L Class A criterion. 

The box-plot depicts the median, 10th, 25th, 75th, and 90th percentiles, and the range. 

Instantaneous DO measurements made at sites in upper Portage Creek, Prairie Creek, and Fish 

Creek met the Class A criterion (Table 18). Of the seven sites in the Portage Creek sub-basin, 

three had DO measurements out of compliance with criteria. All three are located on slow 

winding reaches of Portage Creek after it drops from the plateau to the Stillaguamish River 

floodplain – the same reaches on the 303(d) list. 

Taken together, all DO data collected from 1994 to 2002 at the two lowest sites at 43rd and 212th

appear to show significant improvement. However, a part of the improvement may be the result 

of a shift to collecting samples later in the day that occurred since 1998. Since DO 
Stillaguamish Fecal and DO TMDL Submittal Report Page 71

concentrations tend to increase over the day, measurements taken before noon will usually be 

lower than those taken in the afternoon. Closer investigation showed that some improvement in 

morning DO concentrations was observed in the database. All DO concentrations at 212th

measured before noon in May through November since 1998 were over 5 mg/L; prior to 1998, 

66% were below 5 mg/L. A similar pattern of improvement was seen at 43rd where DO 

concentrations measured before noon since 1998 were an average of 0.8 mg/L higher, and at Fish 

Creek where concentrations were an average of 1.2 mg/L higher. 

The trend is not good when data are examined seasonally. For example, DO concentrations 

taken at 212th from May through November since 1998 have shown a statistically significant 

decreasing trend, similar to the increasing fecal coliform and decreasing temperature trends at the 

same site. The results may suggest that surface flows are decreasing and that ground water is 

becoming a greater portion of the surface flows during these months. Less water may be 

available to handle pollutant loads. Unfortunately, surface discharge data have not been 

collected in the sub-basin to further analyze this theory and determine if there has been 

decreasing summer flows. 

The low DO concentrations and elevated fecal coliform counts do not appear to be correlated, 

but they suggest that pollutant sources are still active in the sub-basin. Land use in the Portage 

Creek sub-basin has been changing. Only one of the seven dairies present in 1996 remains 

active in the lower sub-basin. Residential, non-commercial farm, and commercial developments 

have been increasing on the eastern plateau in and around Arlington. Prairie Creek and upper 

Portage Creek receive storm water through several outfalls that drain the developed areas served 

by Arlington. Also, WSDOT geographic information system coverages (www.wsdot.wa.gov) 

show several stormwater outfalls to Portage Creek from Interstate 5 and Highway 9. The Fish 

Creek watershed on the plateau to the west has also seen increased non-commercial farm and 

residential development activity. 

Portage Creek, March Creek, Twin City Foods Drain #4, Kackman Creek, and the Warm Beach 

Creek set of sites appeared to have chronic DO problems. The 10th percentile DO concentrations 

are well below 8 mg/L. All of these creeks and drains are slow-moving and shallow during the 

low-flow period. All sites are located downstream of areas that are wetlands or have hydric soils 

– potentially influenced by low-DO ground water and anaerobic subsurface water derived from 

riparian wetlands. However, all also have elevated fecal coliform counts (Table 17) and elevated 

nutrient concentrations that may indicate sources of oxygen-demanding wastes are present. 

Manured fields and animal access areas had been sources of contaminants to Portage Creek in a 

1988 – 89 study (Plotnikoff, 1991). Stormwater runoff from Arlington, WSDOT, or Snohomish 

County systems may also be a source of oxygen-demanding pollutants in some of these creeks. 

Warm Beach Creek has similar origins and hydrology to Lake Martha Creek and Unnamed 

Creek #0456 that did not exhibit low DO concentrations. However, the creek has several 

potential sources of oxygen-demanding pollutants just upstream of the WWTP. The horse 

stables and duck pond located on Warm Beach Creek could be sources of manure upstream of 

the WWTP outfall. The Snohomish Conservation District has been working with the Warm 

Beach Conference Center to manage the wastes better at the horse stables. 
Page 72 Stillaguamish Fecal and DO TMDL Submittal Report

The Dike Pond to Warm Beach Slough receives water from the Pasture Drain, effluent from the 

Conference Center WWTP, and Warm Beach Creek. The WWTP discharges an average of 

10 lbs/day of BOD to the creek, sometimes with very little or no dilution. The Pasture Drain 

connects to a network of drains to the north. The low DO concentrations in the Pasture Drain 

could be ground water or nonpoint sources related to agricultural and residential activities. The 

pond retention time is highly variable, and algal respiration, duckweed, and oxygen-demanding 

wastes settled to the bottom probably contribute to reduced water column DO concentrations. 

Salinities in the Pasture Drain and Dike Pond may indicate saltwater inundation. Water density 

differences in the Dike Pond could reduce mixing and aeration. 

Coho salmon and winter steelhead use Portage Creek and Kackman Creek; coho also use March 

Creek (WCC, 1999). Tide gates may prevent fish from entering Twin City Foods Drain #4 and 

the Warm Beach Creek system, and they are not shown as supporting salmon (WCC, 1999). 

Coho spawning and egg incubation occurs from October through May, so the most serious 

periods of depressed DO concentrations may be avoided. Winter steelhead spawning and 

incubation span November through July, so the late incubation period would be most critical for 

attaining adequate DO in these streams. Juvenile salmon using the streams as rearing habitat 

over the year could require refuge elsewhere if DO concentrations drop for extended periods 

below 5 mg/L. 

Monitoring data collected along the two main forks in the upper basin met the Class AA and 

Class A criteria (Table 18). The South Fork Stillaguamish at Granite Falls reach was on the 

303(d) list in 1998. The Stillaguamish Tribe data set for the North Fork Stillaguamish near 

Darrington recorded a low DO measurement prior to 1996, but a single event is not frequent 

enough to qualify for the 303(d) list. The site on the South Fork at Granite Falls in Class AA 

waters met the criterion of 9.5 mg/L, as did the site on the North Fork at Darrington just 

downstream of Class AA waters. The estimated 10th percentile DO concentrations also meet the 

concentration recommended to account for diel minimums within the DO criterion (Table 18). 

Dissolved Oxygen in the Stillaguamish River below Arlington 

The mainstem Stillaguamish River reaches between the confluence of the forks at Arlington and 

Interstate 5 (Figure 7) that were identified as having pre-dawn DO concentrations less than 

8 mg/L in the Earth Tech (1997) study were investigated during this TMDL study. Continuously 

recording probes were deployed in September 2000 and October 2001 to record DO, 

temperature, pH, and conductivity over 48-hour periods. The probes were not deployed in 

August 2000 or 2001 (usually the peak autotrophic growth period) because of mid-summer 

spates (short-duration, high-flow events) and equipment scheduling difficulties. 

Two very different DO conditions were recorded (Figure 18). Where September 2000 DO 

conditions below Arlington were well within the Class A criterion, the October 2001 survey had 

similar DO conditions to the Earth Tech (1997) August 1997 survey (Figure 18 and Table 19). 
Stillaguamish Fecal and DO TMDL Submittal Report Page 73

Stillaguamish River - September 11-13, 2000

8.0

9.0

10.0

11.0

12.0

110000

140000

170000

200000

230000

20000

50000

80000

110000

140000

170000

200000

230000

20000

50000

80000

110000

Time ->

D.O. (mg/L)

RKM 28.5

RKM 24

RKM 21.7

Stillaguamish River - October 2-4, 2001

7.0

8.0

9.0

10.0

11.0

12.0

120000

150000

180000

210000

0

30000

60000

90000

120000

150000

180000

210000

0

30000

60000

90000

120000

151500

Time ->

D.O. (mg/L)

RKM 28.5

RKM 24

RKM 21.7

RKM 17.7

Figure 18. Diel dissolved oxygen (DO) data recorded by probes deployed in the Stillaguamish 

River between Arlington and Interstate 5. Site locations are shown in Figure 7.
Page 74 Stillaguamish Fecal and DO TMDL Submittal Report

Table 19. Comparison of key characteristics during three diel dissolved oxygen (DO) surveys on the 

Stillaguamish River below Arlington. 

Parameter August 1997 September 2000 October 2001 

River Discharge (cfs/cms) 325 / 9.2 2100 / 59.5 605 / 17.2 

Water Temp. range (°C) at RKM 17.3 – 20.4 11.6 – 14.2 11.3 – 14.1 

Photoperiod (hrs) 14.2 12.8 11.5 

DO range (mg/L) at RKM 21.7 7.3 – 11.0 9.4 – 10.1 7.9 – 10.6 

cfs = cubic feet per second; cms = cubic meters per second 

The October 2001 survey confirmed that the pool reach at RKM 21.7 (RM 13) downstream of 

the Arlington WWTP outfall experiences a wide diel DO range, with minimum DO 

concentrations below the 8 mg/L Class A criterion in the early morning hours. The minimum 

DO in 2001 was only 7.9 mg/L compared to 7.3 mg/L in 1997, but the diel DO range in 2001 

was far greater than the upstream and downstream ranges. The cause of the sudden, short-term 

DO loss at the site upstream below Armstrong Creek (RKM 24) around midnight in 2001 is 

thought to be a malfunction of the meter or a temporary interference with the probe. However, 

monitoring the reach for similar responses may be warranted in future studies. 

Water temperatures were lower and there were fewer hours of daylight during the October 2001 

survey than the September 2000 survey. These factors would be expected to impede periphyton 

growth and respiration rates in October. What may have been more important for the DO diel 

range in the pool at RKM 21.7 was that hydrologic conditions were similar in August 1997 and 

October 2001. The discharge volumes in the Stillaguamish River were below 28.32 cms (1000 

cfs) during those surveys compared to over 56.6 cms (2000 cfs) during the September 2000 

survey (Table 19). The channel from Armstrong Creek to the Interstate 5 (I-5) bridge was 

characterized as a series of four slow pools connected by small riffle areas during the two lower 

flow surveys. In both cases, these flow conditions had been stable for more than a week, and 

probably more favorable for supporting periphyton growth. 

Periphyton biomass was not measured directly in August 1997 and September 2000, but 

photographs in the Earth Tech (1997) report show verdant periphyton growth at several key sites. 

The average periphyton biomass (as chlorophyll a) at RKM 19.3 (RM 12) during the October 

2001 survey was estimated at 260 mg/m2

. Some researchers consider biomass concentrations 

greater than 100-200 mg/m2

 to be at nuisance levels (Biggs, 2000; Welch and Dodds, 2000). In 

contrast, a 94.2 cms (3326 cfs) spate had probably scoured away a large portion of the 

periphyton biomass two days prior to the September 2000 diel survey. 

The DO concentrations in the Stillaguamish River are susceptible to the influence of seasonal 

non-filamentous periphyton and filamentous algal growth because ideal light, nutrient, substrate, 

and water velocity and depth are present. During the summer and fall low-flow period, the river 

channel is wide, shallow, and has a range of velocities ideal for both filamentous and nonfilamentous algal growth. The substrate is stable, most commonly having rocks that are cobblesized or greater. Adequate light is present because most of the low-flow channel is not shaded, 

and the turbidity values are minimal in July through September. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 75

Nutrients are supplied from natural watershed sources by recycling processes within the river 

system and from anthropogenic sources. The dissolved forms of nutrients are more available for 

autotrophic algae and periphyton use. Phosphorus appears to be the limiting nutrient for 

periphyton growth based on nitrogen-to-phosphorus (N/P) ratios and QUAL2Kw model 

simulations. Ratios greater than 10:1 generally indicate phosphorus is the limiting nutrient for 

algal biomass growth, and under 10:1 indicates nitrogen limitation. 

The monthly median N/P ratios as dissolved inorganic nitrogen (DIN) to soluble reactive 

phosphorus (SRP) in the South Fork Stillaguamish River (Ecology Station 05A090) was 38:1 to 

143:1 (Ecology, 2002). In the North Fork Stillaguamish River (05B070) the range of ratios has 

been 22:1 to 119:1. At Interstate 5 (05A070), the monthly median ratios of 39:1 to 149:1 are 

greater than 20 throughout the year, and similar to the South Fork ratios. 

Total phosphorus loading into the upper mainstem reaches is important because bacteria can 

mineralize some of the bound phosphorus into more usable forms by autotrophs. Total 

phosphorus concentrations and loads appear to have been increasing since 1980 according to 

trend analyses of data collected by Snohomish County Surface Water Management above 

Arlington (MSAR) and by Ecology at I-5 (05A070), South Fork at Arlington (05A090), South 

Fork at Granite Falls (05A110), and the North Fork at Cicero (05B090) (Figure 19). The total 

phosphorus loads at North Fork at Cicero, South Fork at Arlington, and at I-5 have increased 

without concomitant increases in discharge volumes. Some caution is necessary in interpreting 

phosphorus trend data because the analytical detection limits for phosphorus have changed over 

the past decade. 

Arlington WWTP, several tributaries, and nonpoint sources discharge additional phosphorus to 

the river between the confluence of the forks and Interstate 5. Arlington WWTP effluent is the 

major contributor of phosphorus, especially as SRP, into the reach during the low-flow season. 

Based on the few TMDL synoptic surveys during the summer and fall. 

• 56% to 78% of the total phosphorus load comes from upstream 

• 15% to 33% comes from the Arlington WWTP 

• 1.5% to 2% comes from Armstrong Creek 

• 0.2% comes from March Creek 

• 1.6% to 14% comes from unidentified nonpoint sources or instream sources 

Given the ideal conditions for periphyton growth in the Stillaguamish River, very little 

phosphorus and nitrogen is needed to stimulate periphyton growth to nuisance levels if low flows 

are stable for more than a week. For example, the average periphyton biomass measured as 

chlorophyll a in July 2001 was 88 mg/m2 at the confluence of the two forks at RKM 28.5 

(RM 18) above the Arlington WWTP outfall. The concentration of SRP in the water column 

then was less than 5 ug/L (~ 25 lbs/day), total phosphorus was 12 ug/L (75 lbs/day), and DIN, 

primarily as nitrate, was 72 ug/L (451 lbs/day). The total phosphorus and nitrate concentrations 

are higher than the North Cascades Ecoregion reference levels, but lower than the Puget 

Lowland Ecoregion levels suggested by EPA in Table 8. 
Page 76 Stillaguamish Fecal and DO TMDL Submittal Report Total Phosphorus Load (lbs/day) 

YEAR

 1

 2

10

20

 100

 200

1000

2000

 10000

 20000

100000

ALL SEASONS 

Seasonal Sen Slope

Stand/Crit

79 85 90 95 00 02

SEASONAL KENDALL (SKWOC)

Slope = 2.89511 

Signif 99%

2xP = 0.0039

Figure 19. A graph of the increasing total phosphorus load recorded at the South Fork 

Stillaguamish River at Arlington from 1979 to 2002 (Ecology site #05A090). 

Arlington WWTP phosphorus input was estimated to be about 2 mg/L SRP (13 lbs/day) and 

2.3 mg/L DIN (15.4 lbs/day) during the same survey. The average periphyton biomass measured 

downstream at RKM 19.3 (RM 12) was 151 mg/m2. The nutrients in the water column also 

increased, he SRP concentration was 5 ug/L, total phosphorus was 17 ug/L, and DIN was 

91 ug/L. The increases in periphyton biomass and the water column nutrient increases were 

greater than would have been expected from Arlington WWTP effluent, Armstrong Creek, and 

March Creek. 

Comparing data analysis and QUAL2Kw model simulations to field observations, it appeared 

that the low DO and increased nutrient conditions in the mainstem Stillaguamish pools were 

affected by more complex processes than periphyton biomass production and respiration. 

QUAL2Kw simulations suggested that periphyton growth and biomass influence a part of the 

diel DO range. However, to match the full range of the field data, an additional oxygen demand 

from another process in the model was necessary. Earth Tech (1997) had found it necessary to 

add a sediment oxygen demand factor to make their QUAL2E model simulations match their 

field data. Groundwater input, sediment oxygen demand, decaying periphytic materials, or 

respiration by heterotrophic bacteria in the saturated gravel bed material below or along the river 

channel are possible sources of additional oxygen demand and nutrients. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 77

Some of the channel and valley features of this reach of the Stillaguamish River suggest that the 

interaction between surface water and water in the channel bed may be occurring. The processes 

within the channel bed, called hyporheic processes, have been identified in other parts of the 

Stillaguamish River (Vervier and Naiman, 1992) and in many rivers like it with channels of 

coarse alluvial materials (Naegeli and Uehlinger, 1997; Uehlinger, 2000). The hyporheic zone 

features heterotrophic bacteria communities capable of using oxygen to decompose organic 

materials, much like a trickling filter in a WWTP. As the bacteria break down the organic 

material, they release nitrogen and phosphorus in the dissolved inorganic form. 

QUAL2Kw simulations of the DO data collected in 1997 (Earth Tech, 1997) were run with and 

without the hyporheic functions (Figure 20). When the hyporheic function was added to the 

QUAL2Kw model (Pelletier and Bilhimer, 2004) in the reaches between the first pool at 

RKM 25 and Interstate 5, the DO, pH, and mineralized nutrient simulations fit the field data 

much better. As a verification test, simulations of the October 2001 field data responded in a 

similar way. Several adjustments to respiration, productivity, and hyporheic exchange rates 

different from the 1997 values were necessary to match the water column data that suggested 

these model functions were site and time specific. 

6

7

8

9

10

11

12

13

29 27 25 23 21 19 17

River Kilometer 

DO (mg/L)

With Hyporheic

No Hyporheic

1997 Field Data

Arlington March Creek I-5 Bridge

Figure 20. QUAL2Kw simulations of maximum and minimum dissolved oxygen (DO) profiles in 

the mainstem Stillaguamish River compared to diel DO data collected by Earth Tech in August 

1997. The effect of simulating hyporheic respiration in QUAL2Kw is demonstrated in the dashed 

lines. 
Page 78 Stillaguamish Fecal and DO TMDL Submittal Report

The potential influence of the hyporheic zone to water quality and stream ecology in certain 

systems has just recently been brought out of academics into applied research (Jones and 

Mulholland, 2000). Unfortunately, the quantities of surface water and ground water entering the 

hyporheic zone were not measured in the Stillaguamish River study, and the exact locations of 

where water enters and exits are not known. The rates of bacterial growth and respiration rates 

and nutrient mineralization rates were not measured either. Although the hyporheic model does 

address some questions about the data, there are many uncertainties concerning the heterotrophic 

bacteria functions, and there may be other valid explanations for the processes observed in the 

Stillaguamish. 

The October 2001 diel monitoring results indicate the DO criterion violation may be limited to 

the one pool since DO concentrations in the next pool downstream at RKM 17.7 (RM 11) were 

significantly above 8 mg/L. However, a more extensive area may be affected under critical 

conditions such as experienced during a seven-day, ten-year, low-flow event. Although the DO 

concentrations are not critically low (less than 5 mg/L) in the pool reach at RKM 21.7 (RM 13.5) 

during any of the surveys, they may pose an impediment to aquatic life during critical conditions. 

The riffle and glide reaches upstream and downstream of the pool are essential spawning areas 

for pink and chinook salmon (WCC, 1999). Low DO concentrations have not been documented 

in these reaches. The area is also a rearing area for most of the salmon species present in the 

basin. 

Critical Conditions 

DO critical conditions generally occurred during the summer and fall low-flow season, although 

the mechanisms for the DO decline differed by site. The mainstem critical condition for low DO 

concentrations occurs during a stable low-flow, with both biomass growth and benthal demand 

mechanisms in place. Tributary sites experience depressed DO concentrations as discharge 

volumes decline in the summer and fall. Higher water temperatures that might lower oxygen 

solubility have not occurred at these sites when low DO concentrations have been recorded. 

In the mainstem Stillaguamish River at RKM 21.7, the largest diel ranges accompanied by 

DO minima below 8 mg/L seem to occur when the following situations coincide. 

• Abundant nutrients are available in the water column 

• Discharge decreases for a week or more below 28.32 cms (1000 cfs) so retention time 

through pools increases 

• Water clarity increases allowing increased periphyton growth 

• Periphyton biomass is not interrupted or scoured away or disrupted by spates, e.g., large 

storm events 

• Groundwater inputs, or chemical and gas exchanges from hyporheic and heterotrophic 

bacteria respiration processes, interact with water in pool reaches 

The TMDL capacity of the mainstem to maintain adequate DO concentrations was evaluated at 

the lowest seven-day average flow with an annual ten-year recurrence interval (7Q10) 

approximately 9.38 cms (330 cfs) at the confluence of the forks. The annual 7Q10 statistic for 
Stillaguamish Fecal and DO TMDL Submittal Report Page 79

the Stillaguamish River is slightly lower than the seasonal 7Q10 (10.30 cms) used in the 

temperature TMDL (Pelletier and Bilhimer, 2004) because the annual 7Q10 usually occurs 

sometime from August through October when temperatures may not be at their peak. Under 

7Q10 flow conditions, the critical reaches of river between Arlington and Interstate 5 are steppools with hydrological properties that generate the greatest diel DO range. By coincidence, the 

Earth Tech (1997) DO monitoring survey in August 1997 was conducted during 7Q10 stream 

conditions (9.29 cms). 

The months with the annual 7Q10 flow statistic are appropriate for mainstem DO evaluation for 

other reasons as well. 

• August through October are critical for some salmon using the mainstem for migration, 

spawning, and egg incubation 

• Periphyton biomass would be still capable of higher growth and decay rates with adequate 

light and nutrient levels 

• Reaction rates for biological decomposition would also be higher than average 

• Lower DO saturation would occur with higher river temperatures in late summer conditions 

The TMDL guidelines state that all accessory parameters and point source loads need to be 

adjusted to critical conditions as well (TMDL Workgroup, 1997). Headwater temperature, DO, 

and chemical inputs are set at the appropriate highest or lowest 10th percentile value. Point 

source loads of BOD, total suspended solids, and ammonia are set to the weekly maxima allowed 

under the permit. The modeling inputs for the Stillaguamish River at the confluence of the 

North and South forks, for Arlington WWTP effluent, and for the tributaries used in the DO 

critical condition model simulation are listed in Table 20. The alkalinity of the headwaters is 

also a sensitive parameter in the model. A value of 25 mg/L as CaCO3 was selected (from a 

range of 25 to 35 mg/L) after determining that it was the minimum concentration observed at 

Ecology site 05A070 (at Interstate 5) under low-flow conditions. 

Table 20. Headwater, point source, and tributary input values used to evaluate Stillaguamish River 

dissolved oxygen in the QUAL2Kw model simulations under critical low-flow conditions. 

DO Temp Flow BOD5 NH3-N NO3-N SRP TP Name mg/L ° C cms mg/L mg/L mg/L mg/L mg/L 

Headwater at 

RKM 28.5 

8.5 – 9.6 18 – 22 9.382 2 0.001 0.066 0.005 0.030 

Arlington 

WWTP 

3.0 – 6.0 13 – 20 0.088 

(0.131)* 

45 1 2 3 3.2 

Nonpoint Source 4.0 – 5.0 16 – 20 0.050 35 0.1 5.0 0.5 1.0 

Armstrong 9.0 – 10.5 12 – 14 0.139 4 0.005 0.77 0.017 0.049 

Nonpoint Source 4.0 – 5.0 16 - 20 0.020 35 0.5 1.0 0.1 0.6 

March Creek 4.0 – 5.0 13 – 18 0.016 4 0.010 0.100 0.009 0.050 

Portage Creek 5.0 – 8.0 13 -15 0.234 6 0.005 0.665 0.030 0.078 

Pilchuck Creek 7.9 - 10 15 – 22 0.200 2 0.005 0.550 0.005 0.023 

Glade Bekken 10 – 11 13 – 18 0.027 3 0.005 0.400 0.045 0.093 

* Phase 2 Arlington WWTP discharge volume 

Critical DO conditions at several tributary sites did not appear to be affected by biomass 

production. Depressed tributary DO concentrations may be aggravated by effects from benthal 
Page 80 Stillaguamish Fecal and DO TMDL Submittal Report

demand, oxygen-demanding pollutants from point and nonpoint sources, or inputs from ground 

water or wetlands with low DO concentrations during low-flow periods. Seasonal low flows 

appeared to contribute to the severity of the DO problems in some creeks. 

Summary of Dissolved Oxygen Results 

DO measurements during the 2000-2002 TMDL study period reveal that there are a few reaches 

in some water bodies in the Stillaguamish River basin that experience DO minima below 8 mg/L. 

Most of these reaches are located in smaller tributaries or drains in the lower Stillaguamish River 

floodplain. Data from two mainstem reaches of the Stillaguamish River also did not meet 

criteria. Low DO measurements are more prevalent in the summer/fall low-flow period. DO 

concentrations at several sites appeared to have improved since 1994. 

 

Although the South Fork Stillaguamish River above Granite Falls was previously listed on the 

1998 303(d) list, it appears to have been meeting Class AA (minimum of 9.5 mg/L) criteria since 

1995. Data from 12 water body reaches did not meet the DO criterion for Class A waters 

(minimum of 8.0 mg/L). Portage Creek and the lower Stillaguamish River (RM 3) were on the 

1998 303(d) list. The 12 sites are: 

• Twin City Foods Drain #4 

• Warm Beach Creek above the Warm Beach WWTP outfall 

• Agricultural Pasture Drain to Warm Beach Dike Pond 

• Warm Beach Dike Pond to Warm Beach Slough 

• Pilchuck Creek at Jackson Gulch Road 

• Portage Creek at 212th NE 

• Portage Creek at 15th NE 

• Portage Creek at 43rd NE 

• March Creek from mouth to 220th NE 

• Kackman Creek at 252nd NE 

• Stillaguamish River at RKM 21.7 (RM 13.5) 

• Stillaguamish River at the bifurcation with the Old Stillaguamish Channel at RKM 4.8 

(RM 3) 

The lowest DO oxygen concentrations at all sites were reported from measurements made during 

the months of May through October. Several of the sites with low DO were measured in small 

streams with slow-moving reaches located in the floodplain. In addition to possible 

anthropogenic sources of oxygen demand, low-DO ground water, wetlands drainage, and 

hyporheic zone processes may naturally depress instream DO concentrations below 8 mg/L 

during the low-flow period. 

It is likely that DO concentrations around Stillaguamish River RKM 4.8 (RM 3) occasionally fall 

below the Class A criterion because the Old Stillaguamish River Channel reverses flow and 
Stillaguamish Fecal and DO TMDL Submittal Report Page 81

discharges low-DO water back into the main channel during some tidal cycles under low-flow 

conditions. DO conditions in the reach may improve if a tide gate installed on the Old 

Stillaguamish Channel prevents the reverse flow into the Stillaguamish River. 

The situation at RKM 21.7 (RM 13.5) of the Stillaguamish River is more complex and involves 

periphyton growth and hyporheic respiration or some other mechanism. The DO minima below 

8 mg/L have been recorded in one pool reach after low-flow conditions have been maintained for 

more than a week. The Arlington WWTP, upper basin inputs, tributaries, and other potential 

sources of nutrients and BOD upstream of the reach may aggravate the DO depression. 

pH 

Current Conditions and Trends 

 

Mainstem Stillaguamish River was listed for pH on the 1996 303(d) list based on three 

excursions beyond the standard at the Ecology long term monitoring station 05A070 at I-5 

bridge, in October 1987, December 1989, and January 1990. In subsequent years prior to data 

review for the 1998 303(d) list, there were no further impairments, so this was not included on 

the 1998 list. For this study, additional samples in this reach were collected at TMDL stations 

05TMS11 and 05TPILUP during 2001; no pH excursions were measured (Ecology August 

2004); therefore, as noted in Table 8, this evaluation recommends delisting this reach for pH. 

The South Fork Stillaguamish River was the only water body in the basin on the 1998 303(d) list 

as pH-impaired. The listing was based on two Ecology instantaneous measurements in the 

South Fork at Arlington recorded in 1987 and 1991 (Ecology, 2000). The pH values were lower 

than the 6.5 standard units (s.u.) Class A criterion (6.4 s.u. on both occasions). The pH 

measurements taken at the site have not fallen below 6.5 s.u. since 1991 (Figure 21). 

One reason for the apparent improvement may be that the monitoring time changed in 1993 from 

the morning to the afternoon. As with dissolved oxygen, pH values tend to increase in the 

afternoon and decrease at night in response to aquatic production and respiration. However, the 

data still meet the criterion after applying a 0.2 s.u. safety factor to the 10th percentile statistic to 

account for estimating maximum pH values based on instantaneous measurements (see 

Analytical Framework). Another reason may be that an event or instream condition was 

monitored that has not occurred during any monitoring run since. For example, a source of 

stormwater upstream of the site may have been eliminated. And finally, pH is not easily 

measured in low-conductivity water. Low-ionic buffers and better liquid-filled probes were not 

used by Ecology until the mid-1990s when quality control measures became stricter. Since these 

changes, there is higher confidence in the accuracy of the pH measurements. 

Ecology and Snohomish County collected a combination of instantaneous and diel pH 

measurements throughout the basin during the 2000-2002 TMDL study period. The 

Stillaguamish Tribe stopped measuring pH at its sites in 1999 (Klopfer, 2000). Most of the pH 

measurements were taken throughout the Stillaguamish River basin in the same manner as the 

dissolved oxygen measurements. These instantaneous measurements exhibit the same 

limitations for interpretation as the dissolved oxygen measurements; i.e., the diel minima and 
Page 82 Stillaguamish Fecal and DO TMDL Submittal Report

maxima in productive systems usually occur very early in the morning and late in the afternoon 

or early evening. 

A summary of data for 27 sites is presented in Table 21. The calculated 90th and 10th percentile 

values are listed in the table as well. As previously explained, the percentile values are used to 

apply a 0.2 s.u. safety factor to estimate the maximum diel range in highly productive systems. pH

WATER YEAR

 6.0

 6.5

 7.0

 7.5

 8.0

 8.5

80 85 90 95 00 02

WQ Standard 

WQ Standard 

(12)

(12)

(12)

(12)

(12)

(12) (9) (12)

(12) (8) 

(12)

(12)

(12)

(11)

(12)

(12)

(12)

(11) (12)

(12)

(9) 

Figure 21. Monthly pH statistics from the South Fork Stillaguamish River at Arlington (Ecology 

05A090) from 1980 to 2000 shown as a box-plot. Class A pH criteria are shown. The box-plot 

depicts the median, 10th, 25th, 75th, and 90th percentiles, and the range. The number of samples 

used for each box is in the parenthesis above the box. 

The pH data collected by Ecology and Snohomish County monitoring programs suggest low pH 

may be a problem at several sites in the basin. Sites reporting pH measurements below 6.5 s.u., 

or 10th percentile values below 6.7 s.u., were as follows: 

• Stillaguamish River above Arlington below the confluence of the North and South forks 

• Kackman Creek 

• Pilchuck Creek at Jackson Gulch 

• March Creek 

• South Fork Stillaguamish River at Granite Falls 
Stillaguamish Fecal and DO TMDL Submittal Report Page 83

The Stillaguamish Tribe monitoring program also had reported low pH values at Pilchuck Creek, 

Portage Creek, the South Fork Stillaguamish River at Jordan bridge, the North Fork 

Stillaguamish at Whitman bridge, and at Swede Haven bridge prior to 1996. None of the sites 

had had pH values under 6.5 s.u. from 1996 to 1999. The tribal program stopped measuring pH 

at some of the sites in 1999 (Klopfer, personal communication, 2002). 

Table 21. Summary of instantaneous pH measurements made in the Stillaguamish River basin by 

Ecology, Snohomish County, and the Stillaguamish Tribe from June 2000 to June 2002. 

Site 

Number 

of 

Samples 

Concentration 

Range 

(standard units) 

10th and 

90th 

Percentile 

Church Creek at Park 30 7.0 – 7.9 7.1 7.8 

Hat Slough at Marine Drive 43 6.5 – 7.8 6.9 7.5 

Glade Bekken at Silvana Terrace Road 32 6.8 – 7.9 7.1 7.6 

Pilchuck Creek at Jackson Gulch Road 38 6.5 – 8.1 6.6 7.5 

Portage Creek at 212th 33 6.6 – 7.6 6.8 7.3 

Portage Creek at 43rd 25 7.0 – 7.5 7.1 7.4 

Fish Creek 24 6.6 – 7.8 6.8 7.6 

Stillaguamish River at Interstate 5 38 6.9 – 7.8 7.1 7.7 

March Creek at 220th NE 6 6.5 – 7.2 6.5 7.2 

Armstrong Creek at Mouth 3 7.4 – 7.5 7.4 7.5 

Kackman Creek at 252nd 6 6.2 -7.6 6.3 7.2

Armstrong Creek at Hatchery 6 6.8 – 7.7 6.9 7.5 

Stillaguamish River above Arlington 32 6.4 – 7.7 6.9 7.6 

S.F. Stillaguamish at Arlington 42 7.0 – 8.4 7.1 7.8 

Jim Creek at Mouth 4 6.9 – 7.4 7.0 7.3 

S.F. Stillaguamish at Jordan Walkway 12 6.6 – 8.1 6.9 7.9 

S.F. Stillaguamish at Granite Falls 30 6.4 – 8.1 7.1 7.8 

N.F. Stillaguamish at Twin Rivers 13 6.9 – 8.2 7.0 7.9 

N.F. Stillaguamish at Cicero 33 7.0 – 8.2 7.0 7.8 

N.F. Stillaguamish at Whitman bridge 10 6.9 – 8.3 6.9 8.3

N.F. Stillaguamish at C-Post bridge 5 6.9 – 7.6 6.9 7.4 

N.F. Stillaguamish at Darrington 25 7.0 – 8.0 7.3 7.6 

The low pH value of 6.4 s.u. recorded by Ecology at the South Fork Stillaguamish below Granite 

Falls occurred on the first day of monitoring during the November 2001 storm event monitored 

during this TMDL. The next day of the storm event the pH was 7.05 s.u. Storm water from 

Granite Falls could be of some concern here. However, since only one pH violation of criterion 

was detected in the reach (including Ecology site 05A110), it does not qualify under the 303(d) 

listing criteria (Ecology, 2002). Additional monitoring should be considered during storm 

events, but actions through a TMDL are not warranted at this time. 

High pH values, over 8.5 s.u., were not reported at any site during the 2000-2002 TMDL study 

period, although pH values above 8.0 were recorded at several sites on the North and South 

forks. The 90th percentile pH value for the North Fork at Whitman bridge of 8.3 s.u. was at the 

safety factor for productive systems. The high pH values were recorded on three consecutive 

weeks in August 2000 during the TMDL recreation beach bacteria survey (Coffler, Gridley, and 

Joy, 2004). The samples were all collected in the late morning or early afternoon, whereas pH 

maxima usually occur in the late afternoon or early evening. 
Page 84 Stillaguamish Fecal and DO TMDL Submittal Report

The low buffering capacity (low alkalinity) of the system could make it susceptible to swings in 

pH over acceptable levels. In past years, the Stillaguamish Tribe documented high pH values in 

the North Fork and other sites in the basin (Klopfer, 2000). Periodically during summer lowflow conditions, Ecology site 05B070, the North Fork Stillaguamish River at Cicero, has 

recorded pH values greater than 8.5 s.u. along with supersaturated dissolved oxygen 

concentrations in 1997 and 1999 (Ecology, 2003a). 

The channel and hydrological characteristics of the North Fork are as ideal as the mainstem for 

periphyton growth. Total phosphorus concentrations on the North Fork have not shown 

significant increases since 1994, but they may have increased since the 1980s; the data quality 

from the earlier period is not high. However, an increase in periphyton biomass production 

stimulated by nutrients in a poorly-buffered system could cause seasonal episodes of the elevated 

pH levels. As the periphyton grow, they use carbon and shift the carbonate balance from acidic 

to basic pH values. During respiration processes at night, the shift is back from basic to acidic 

pH values. 

The lowest pH values at most sites throughout the basin usually occurred in November through 

April. Senescing organic matter washing through or into the stream and river channels could 

create declining pH as bacteria decompose the organic material; western Washington rainwater 

(median pH ~ 5.3) could be another source. Some of the low pH values (5.2 – 6.3 s.u.) recorded 

by the Stillaguamish Tribe throughout the basin in 1994 and 1995 were measured during storm 

events (Klopfer, 2000). 

The low pH values reported by Snohomish County at the Stillaguamish River above Arlington 

occurred during storm events. Low pH values were more common at this site from 1999 to 2000 

(Snohomish County, 2002). The 10th percentile value for 49 pH data collected from 1999 to 

2002 is 6.6. Random sampling that include more storm events in one year, changes in upstream 

water quality, or changes in measuring technique can influence the data and statistics. Arlington 

and Washington Department of Transportation (WSDOT) have stormwater outfalls upstream of 

the site on the South Fork. The site qualifies for the 303(d) list and will have allocations based 

on stormwater contributions. 

The pH values recorded at a few tributary sites (Pilchuck, Kackman, March) are low enough to 

require closer scrutiny. As mentioned in the dissolved oxygen discussion, Pilchuck Creek and 

March Creek have Snohomish County and WSDOT stormwater outfalls upstream of the 

monitoring sites. The low pH values have been recorded during winter months of the year when 

organic decomposition processes rather than instream productivity may be active. 

It is uncertain how much local wetlands, groundwater input, and hydric soils contribute to the 

low pH values, and how much can be attributed to waste inputs. At all, except Pilchuck Creek, 

elevated fecal coliform counts and nutrient concentrations accompanied the low pH. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 85

Groundwater pH values in the areas of interest have ranges of 6.0 to 8.6 s.u., depending upon the 

aquifer source. For example, water to the Portage Creek basin that runs through the Vashon 

recessional outwash aquifer has a median pH value of 6.2 s.u. (Thomas, Wilkinson, and Embrey, 

1997). 

A majority of pH values measured at Kackman Creek have been below 6.5 s.u. Stillaguamish 

Tribe pH monitoring data from 1996 to 1999 and six of Ecology’s 2000- 2001 TMDL surveys 

suggested low pH values are common at the site. The TMDL monitoring occurred during or 

shortly after storm events, but discharge volumes were less than 0.14 cms (5 cfs). The 

Stillaguamish Tribe monitoring reported that low pH values occurred during November through 

May. Kackman Creek also experiences chronic low dissolved oxygen concentrations during 

storm events and summer low-flow periods; fecal coliform counts seem to be related to storm 

events. Ground water with low pH would be a source during a dry winter season in Kackman 

Creek. Upstream wetlands, agricultural sources, and stormwater could also be sources in wetter 

periods. 

Critical Conditions 

The critical hydrologic and biological conditions for high pH in Stillaguamish freshwater 

systems would occur during the same season as for low dissolved oxygen (August to October). 

The potential for elevated pH at some sites in the Stillaguamish basin would most likely be a 

result of biomass production during low flow during the growing season. Nutrients, light, and 

substrate are limiting factors for periphyton growth and its effect on pH. The alkalinity and 

carbon cycling of the water body is another controlling factor for pH. The North Fork 

Stillaguamish at Whitman bridge was the only site reporting a potential high pH problem, but 

ambient monitoring data suggests there may be pH problems downstream to Cicero during 

low-flow conditions. 

Low pH values in parts of the basin occurred during the winter, especially during storm events 

but also during low-flow periods. The critical conditions causing a depressed pH response may 

be from an influx of low pH water and oxygen-demanding substances of natural or 

anthropogenic origin. Anthropogenic and natural sources can contribute during low-flow 

conditions or during storm events. 

Summary of pH Results 

The pH-limited 303(d)-listed site, South Fork Stillaguamish River at Arlington, has met criteria 

since 1991 according to Ecology monthly monitoring data and data collected during the TMDL 

monitoring surveys. Two sites have had unacceptable pH measurements below the 6.5 s.u. 

criterion. 

• Stillaguamish River above Arlington had low pH values associated with storm events. 

• Kackman Creek at 252nd had low pH at all times of the year. Natural and anthropogenic 

sources may be contributing to the low values. 
Page 86 Stillaguamish Fecal and DO TMDL Submittal Report

A 0.2 s.u. safety value is applied to the 10th and 90th percentile pH statistics to estimate diel 

minima and maxima caused by instream productivity or other factors. The statistics at three sites 

did not meet the safety value categories. 

• The North Fork Stillaguamish from Whitman bridge to Cicero may have maximum pH 

values greater than 8.5 s.u. from biomass productivity. 

• March Creek may have low pH values resulting from stormwater runoff, wetland drainage, 

ground water, and nonpoint source pollutants. 

• Pilchuck Creek may have low pH values from stormwater runoff, decomposing materials 

delivered to the water bodies from nonpoint sources, or instream decomposition processes. 

Storm events in November through April are associated with lower pH values in the river and 

several streams in the basin. Low-pH rainwater, subsurface flow through hydric soils and 

wetlands, and surface stormwater pollutants are possible sources of the decreased pH. The 

impact of storm water and nonpoint sources need to be identified and controlled. 

Arsenic and Mercury 

Current Conditions - Arsenic 

The 1998 303(d) listing for arsenic in the Stillaguamish River was initially from data in the 

Ecology database that was coded improperly; no detectable concentrations of arsenic were 

reported at the Stillaguamish River at Interstate 5 (Ecology 05A070) between 1991 and 1996. 

Recently, better methods have been developed to analyze arsenic in natural waters. Using these 

low-detection limit methods, Johnson (2002) demonstrated that arsenic is commonly detected in 

Washington State rivers at concentrations less than those causing acute or chronic aquatic 

toxicity, but greater than the human-health criteria based on a 1:1,000,000 carcinogenic risk. 

Ecology sampled several sites in the Stillaguamish River basin for total recoverable and 

dissolved arsenic in 2000 and 2001. The sampling focused on the North and South forks near 

their confluence and the mainstem at I-5 and at Marine Drive (Table 22). In addition, Arlington 

WWTP effluent was sampled three times, and Portage Creek was sampled once. 

Table 22. Total recoverable (TR As) and dissolved (Diss. As) arsenic concentrations and total 

suspended solids (TSS) concentrations collected from sites on the Stillaguamish River 

during Ecology’s TMDL surveys. 

North Fork 

Stillaguamish River* 

South Fork 

Stillaguamish River 

at Confluence 

Stillaguamish River 

at Interstate 5 

Hat Slough at 

Marine Drive 

Date 

TR 

As 

ug/L 

Diss. 

As 

ug/L 

TSS 

mg/L 

TR As. 

ug/L 

Diss. 

As 

ug/L 

TSS 

mg/L 

TR 

As. 

ug/L 

Diss. 

As 

ug/L 

TSS 

mg/L 

TR 

As. 

ug/L 

Diss. 

As 

ug/L 

TSS 

mg/L 

10/5/00 - - - 0.5 U 0.5 U 14 - - - 0.5 U 0.5 U 4 

1/31/01 1.1 0.38 31 4.1 0.5 335 2.4 0.8 187 2.7 0.95 164 

5/8/01 0.43 0.4 5 0.44 0.39 10 0.6 0.37 9 0.47 0.41 9 

6/12/01 1.02 0.42 78 3.27 0.55 524 1.4 0.44 203 0.82 0.45 40 

7/12/01 0.75 0.78 2 0.68 0.63 9 0.67 0.67 4 0.65 0.65 2 
Stillaguamish Fecal and DO TMDL Submittal Report Page 87

North Fork 

Stillaguamish River* 

South Fork 

Stillaguamish River 

at Confluence 

Stillaguamish River 

at Interstate 5 

Hat Slough at 

Marine Drive 

Date 

TR 

As 

ug/L 

Diss. 

As 

ug/L 

TSS 

mg/L 

TR As. 

ug/L 

Diss. 

As 

ug/L 

TSS 

mg/L 

TR 

As. 

ug/L 

Diss. 

As 

ug/L 

TSS 

mg/L 

TR 

As. 

ug/L 

Diss. 

As 

ug/L 

TSS 

mg/L 

10/3/01 0.96 0.91 12 0.84 0.8 - 0.88 0.81 6 - - - 

10/16/01 0.7 0.65 5 0.61 0.53 18 0.67 0.56 15 0.66 0.55 11 

* Samples were collected at confluence on 6/12 and 10/3; all others were collected at the Cicero monitoring site. 

U = not detected at the concentration listed 

ug/L = microgram/liter 

mg/L = milligram/liter 

The values in the table are total recoverable and dissolved arsenic. Organic and inorganic 

arsenic were not speciated in the samples. The dissolved fraction of arsenic was about 80% to 

100% of the total recoverable fraction except during storm events with higher total suspended 

sediment (TSS) concentration, e.g., on 1/31/01 and 6/12/01 when dissolved arsenic was 15% -

60% of the total fraction. As observed elsewhere in the state, none of the concentrations exceed 

the aquatic toxicity criteria in Table 6. However, all the data are in violation of the National 

Toxics Rule (40 CFR 131.36) (NTR) human-health criteria. 

Total recoverable arsenic concentrations were generally higher in the South Fork than in the 

North Fork Stillaguamish, but no significant difference was observed between dissolved arsenic 

concentrations from the two forks. Arsenic concentrations remained unchanged down the 

mainstem Stillaguamish River between I-5 and Marine Drive. Arlington WWTP effluent total 

recoverable arsenic was consistently around 0.85 ug/L (range 0.83 – 0.91 ug/L), similar to 

average concentrations in the North and South forks. Portage Creek, sampled during the June 

2001 storm event had a total arsenic concentration of 2.73 ug/L, similar to the concentration of 

arsenic sample collected from the South Fork on that day (Table 22). 

Two other independent monitoring studies with data pertinent to arsenic in the Stillaguamish 

basin were conducted during the TMDL evaluation period. Johnson (2002) sampled and 

evaluated water column concentrations of arsenic from several sites in Washington. Among 

those rivers sampled were the North Fork Stillaguamish near Darrington and the Stillaguamish 

River at Silvana (Table 23). 

 

Table 23. Total recoverable arsenic (TR As), total suspended solids (TSS), and flow data at two sites 

in the Stillaguamish River basin (Johnson, 2002). 

NF Stillaguamish near Darrington (05B110) Stillaguamish River at Silvana (05A070) 

Date TR As 

 (ug/L) 

TSS 

(mg/L) 

Flow 

(cfs) Date TSS (mg/L) 

TR As 

(ug/L) 

Flow 

 (cfs) 

7/17/01 0.75 0.5 72 7/17/01 9 0.41 1090 

8/21/01 0.68 0.5 41 8/22/01 279 2.65 4278 

9/18/01 0.69 1 41 9/19/01 2 0.93 488 

10/23/01 1 201 1549 10/23/01 588 1.6 17215 

11/14/01 1.5 284 6909 11/14/01 1290 2.48 26322 

12/11/01 0.27 2 405 12/11/01 56 0.99 3893 

1/22/02 0.23 2 - 1/22/02 47 0.88 3808 
Page 88 Stillaguamish Fecal and DO TMDL Submittal Report

NF Stillaguamish near Darrington (05B110) Stillaguamish River at Silvana (05A070) 

2/27/02 2.03 16 706 2/27/02 27 0.7 5281 

3/19/02 0.3 2 366 3/19/02 15 0.57 3551 

4/23/02 0.22 4 597 4/22/02 59 0.78 3422 

5/22/02 0.21 3 706 5/22/02 11 0.41 7674 

6/19/02 0.19 6 533 6/19/02 11 0.37 6774 

Johnson’s (2002) arsenic concentrations at the Stillaguamish River at Interstate 5 (Silvana) are 

similar to those detected during the TMDL surveys. Just as in the TMDL surveys, the arsenic 

concentrations in Johnson’s samples increased during storm events and as TSS increased. Based 

on the concentrations found in rivers in Washington State and in other background sources like 

rainwater, Johnson concluded that typical river concentrations of arsenic would not meet the 

NTR human-health criteria. He recommended that most of the Section 303(d) listings for arsenic 

be removed, and that future listings should clearly define an anthropogenic source. 

Abandoned and inactive mines in the upper basin may be of some concern as a potential source 

of arsenic contamination. Raforth, Norman, and Johnson (2002) sampled Glacier Creek above 

and below an abandon mine in the Monte Cristo District. The mine is not located in the South 

Fork Stillaguamish River sub-basin, but it is just over the ridge in the South Fork Sauk River. 

The concentrations of total recoverable arsenic in Glacier Creek above and below the waste rock 

dump area were greater than 0.3 ug/L. Loading analysis revealed that the concentration coming 

from a combination of the waste rock dump area and two tributaries was approximately 

11 – 12 ug/L arsenic. Stream sediment samples also were enriched upstream and downstream of 

the waste rock dump when compared to quality guidelines (Raforth, Norman, and Johnson, 

2002). 

Ground water is another potential source of arsenic in the Stillaguamish basin. The median total 

arsenic concentration for 295 groundwater samples collected in the western part of Snohomish 

County by USGS in 1993 and 1994 was 2 ug/L (Thomas, Wilkinson, and Embrey, 1997). 

Fifty-two wells, representing all seven geohydrologic units, had total arsenic concentrations 

greater than 10 ug/L. Five samples exceeded the EPA drinking water standard for arsenic of 

50 ug/L. All five were taken from wells located between Granite Falls and Arlington. 

Based on the five TMDL monitoring events with data from all four sites, the average arsenic 

load delivered from the two forks accounted for approximately 80% of the average arsenic load 

calculated for Marine Drive. This was similar to the percentage of discharge delivered from the 

upper basins. Grouping results from all TMDL sites, TSS concentrations appeared to be 

correlated with total recoverable arsenic concentrations even though most of the arsenic was in 

the dissolved form at low TSS concentrations (Figure 22). The strong correlation between TSS 

and arsenic at the grouped sites suggest that source materials of arsenic and TSS are probably the 

same. 

Arsenic concentrations above the human-health criteria appear to be in all compartments of the 

Stillaguamish basin hydrology. The arsenic loading estimates, groundwater testing, and the 

arsenic and TSS analyses indicate that source materials of arsenic are the same throughout the 

basin. The limited number of available data suggests that no arsenic enrichment takes place 
Stillaguamish Fecal and DO TMDL Submittal Report Page 89

between these upper and lower basin sites. Enrichment from abandoned and inactive mines in 

the upper basin was not detected. The South Fork Stillaguamish River had slightly higher 

concentrations of arsenic than the North Fork, and there were more mines in the South Fork 

sub-basin with yields of arsenic (Huntting, 1956). However, groundwater concentrations from 

wells in the South Fork basin were higher than other areas (Thomas, Wilkinson, and Embrey, 

1997). 

y = 0.6843e0.0041x

R2 = 0.7393

0

1

2

3

4

5

6

7

1 10 100 1000

TSS (mg/L)

As (ug/L)

Figure 22. Correlation between water column total suspended solids (TSS) concentrations and 

total recoverable (TR) arsenic concentrations from samples collected at sites in the Stillaguamish 

River basin: North Fork Stillaguamish at Cicero and Twin Rivers, South Fork Stillaguamish at the 

mouth, Stillaguamish River at Interstate 5 (I-5), and Hat Slough at Marine Drive. 

Current Conditions - Mercury 

Mercury was investigated because two samples collected at the Stillaguamish River at I-5 

(Ecology 05A070) in 1995 had concentrations greater than the freshwater aquatic chronic 

toxicity criterion of 0.012 ug/L. Both samples had accompanying TSS and turbidity values that 

were elevated, and river flows were greater than 141.6 cms (5000 cfs). One of the mercury 

results did not meet quality assurance criteria, so no 303(d) listing for mercury was made based 

on these samples. 
Page 90 Stillaguamish Fecal and DO TMDL Submittal Report

During the TMDL surveys, samples were collected for total mercury at the same times and sites 

as arsenic. The total mercury results are shown in Table 24. Most results met aquatic toxicity 

and human-health criteria. However, samples collected at most sites during storm events on 

1/31/01 and 6/12/01 did not meet the 0.012 ug/L freshwater chronic toxicity criterion. The 

criterion is a four-day average, so it is unknown if the criterion was actually violated during the 

two events. 

Table 24. Total recoverable mercury concentrations (ug/L) collected from sites on the 

Stillaguamish River during Ecology’s TMDL surveys. (Total suspended solids concentrations 

associated with these samples are shown in Table 22.) 

Date North Fork 

Stillaguamish River * 

South Fork 

Stillaguamish River 

at Confluence 

Stillaguamish River 

at Interstate 5 

Stillaguamish River 

at Marine Drive 

(Hat Slough) 

10/5/00 - 0.0021 - 0.002 U 

1/31/01 0.0063 0.0261 J 0.0217 J 0.0216 J 

5/8/01 0.0034 0.0029 0.003 0.0046 

6/12/01 0.016 0.0497 0.019 0.01 

7/12/01 0.002 U 0.0025 0.0026 0.0036 

10/3/01 0.0032 0.0029 0.0043 

10/16/01 0.0054 0.0059 0.0064 0.0076 

* Samples were collected at confluence on 6/12 and 10/3; all others were collected at the Cicero monitoring site. 

U = not detected at the concentration listed. 

J = estimated concentration 

Bold values exceed the freshwater aquatic chronic toxicity criterion of 0.012 ug/L. 

Mercury appeared to be correlated with arsenic and TSS. Mercury concentrations were highly 

correlated with arsenic concentrations at Hat Slough, I-5, and the South Fork (Figure 23). The 

North Fork correlation was not as strong. The correlation between mercury and TSS suggests 

that suspended sediment may be the source of the mercury (Figure 24). Mercury increased with 

increased TSS and increasing discharge volumes during storm events. 

Based on the five monitoring events with data from all four sites, the average mercury load 

delivered from the two forks accounted for approximately 50% of the average mercury load 

calculated for Marine Drive. This was different from the arsenic loading analyses. The results 

might suggest that a higher proportion of mercury was generated in the lower basin than in the 

upper basin based on drainage area, but the source of mercury is unknown. The data were not 

consistent in showing if the gain in mercury occurred between Arlington and I-5, or between 

I-5 and Hat Slough. However, the key to controlling mercury concentrations does appear to be 

controlling TSS concentrations. 

Mercury samples were collected from Arlington WWTP effluent and Portage Creek during the 

2000-2002 TMDL study period. The three Arlington WWTP effluent samples analyzed for 

mercury had concentrations from 0.0034 to 0.0096 ug/L. These concentrations are similar to the 

average concentrations in the North and South forks of the Stillaguamish (Table 24). The 

mercury sample collected from the effluent on June 12 was 0.0034 ug/L, far lower than the river 
Stillaguamish Fecal and DO TMDL Submittal Report Page 91

mercury concentrations at that time. Portage Creek was sampled during the June 2001 storm 

event. The mercury concentration of 0.018 ug/L was similar to the mainstem Stillaguamish 

River at I-5 during that event. Both were greater than the 0.012 ug/L aquatic toxicity criterion 

and contained high TSS concentrations. 

0.001

0.01

0.1

0.1 1 10

TR Arsenic (ug/L)

Hg (ug/L)

SF I-5 Hatt NF

Figure 23. Correlations between total recoverable arsenic (TR Arsenic) and mercury (Hg) in 

whole water samples from four sites in the Stillaguamish River basin: North Fork Stillaguamish at 

Cicero and Twin Rivers (NF, r2

=0.23), South Fork Stillaguamish at the mouth (SF, r2=0.73), 

Stillaguamish River at Interstate 5 (I-5, r2

=0.89), and Hat Slough at Marine Drive (Hatt, r2=0.93). 
Page 92 Stillaguamish Fecal and DO TMDL Submittal Report

y = 0.0011x0.5704

R2 = 0.8269

0.001

0.01

0.1

1

1 10 100 1000

TSS (mg/L)

Hg (ug/L)

Chronic toxicity criterion

Figure 24. Relationship between total suspended solids (TSS) and mercury (Hg) concentrations 

for samples collected in the Stillaguamish River basin. The 0.012 ug/L chronic aquatic toxicity 

criterion for mercury is shown. 

Mercury was also collected quarterly in 2002 by Ecology’s monitoring program at the North 

Fork Stillaguamish near Darrington (05B110). One of four samples did not meet the freshwater 

chronic toxicity criterion (Table 25). 

Table 25. Quarterly mercury, total suspended solids, and discharge data collected in 2002 from 

Ecology site 05B110, North Fork Stillaguamish River near Darrington. 

Date Mercury (ug/L) TSS (mg/L) Discharge (cfs) 

02/27/02 0.015 16 706 

04/23/02 0.0048 4 597 

06/19/02 0.0032 6 533 

08/21/02 0.0020 1 111 

Mercury concentrations were elevated in the February sample during a moderate flow event, 

five days after a storm (USGS records for North Fork Stillaguamish near Arlington). The TSS 

concentration of 16 mg/L was in the upper quartile of monthly measurements taken near 

Darrington since 1992. 

The sources of mercury in the upper watershed are similar to those for arsenic, and are found in 

several compartments of the basin hydrology. Abandoned and inactive mines in the upper basin 

may be of some concern as a potential source of contamination. The concentration of total 

mercury in Glacier Creek (in the Sauk River basin) above the waste rock dump area was 
Stillaguamish Fecal and DO TMDL Submittal Report Page 93

0.0042 ug/L during a high-flow condition, and less than the detection limit of 0.002 ug/L during 

a low-flow condition (Raforth, Norman, and Johnson, 2002). The downstream concentrations 

increased to 0.0058 ug/L during the high-flow event; no mercury was detected during the 

low-flow condition. 

Loading analysis of the Glacier Creek data revealed that the concentration coming from a 

combination of the waste rock dump area and two tributaries was approximately 0.006 ug/L 

mercury. Stream sediment samples also were enriched upstream, but not downstream, of the 

waste rock dump when compared to quality guidelines (Raforth, Norman, and Johnson, 2002). 

 

Another potential basin-wide source of mercury is rainwater. Rainwater samples collected in 

Washington by the National Atmospheric Deposition Program in 2001 contained an average 

concentration of 0.006 ug/L mercury. This concentration is higher than many of the values in 

Table 24. 

Ground water is another potential source of mercury in the Stillaguamish basin. Mercury 

concentrations (0.2 - 1.2 ug/L) were detected by USGS in three wells in the Stillaguamish basin 

at a reporting limit of 0.1 ug/L (Thomas, Wilkinson, and Embrey, 1997). The EPA drinking 

water limit for mercury is 2 ug/L. Two of the samples were from wells near Stanwood; the other 

was from a well in the North Fork Stillaguamish River basin. The source of mercury in these 

samples was not discerned. 

Fish collected in Port Susan have shown detectable, but not elevated, mercury tissue burdens 

(West, O’Neill, Lippert, and Quinnell, 2001). Mercury was detected in all three English sole 

collected in Port Susan. Concentrations were 0.06 to 0.07 mg/Kg, far below the 1.0 mg/Kg 

action level for mercury. 

Critical Conditions – Arsenic and Mercury 

Total recoverable arsenic and mercury concentrations were highest during high-flow conditions 

accompanying elevated suspended solids concentrations. Arsenic and mercury loads were highly 

correlated with TSS loads. Arsenic concentrations are consistently greater than the EPA humanhealth criteria, so no condition is more critical than another to meet these criteria. Reducing TSS 

may reduce arsenic concentrations, but not to levels below the criteria. Mercury concentrations 

only exceeded the freshwater chronic toxicity criterion during storm events. Therefore, storm 

events producing high TSS over more than four days would be a critical condition for mercury 

loading and chronic criteria violations. 

Summary of Arsenic and Mercury Results 

 

Arsenic concentrations in the Stillaguamish River basin are typical for Washington State waters, 

i.e., they are high enough to violate human-health criteria based on carcinogenic risk, but are far 

below levels harmful to aquatic organisms. Water column arsenic appears to be in the dissolved 

form except when elevated TSS concentrations are present. There is a high correlation between 
Page 94 Stillaguamish Fecal and DO TMDL Submittal Report

arsenic loads and TSS loads at all sites. The regressions and loading comparisons appeared to 

show that there was no arsenic enrichment in the lower basin, and that arsenic was distributed 

evenly throughout the basin. The contributions of abandoned and inactive mining areas and 

ground water are not known. 

Mercury concentrations in the Stillaguamish basin were below criteria except during two storm 

events. It is unknown if mercury concentrations exceed the chronic toxicity criteria for aquatic 

life over four consecutive days. Most storm events in the basin are of a shorter duration. 

Mercury loads are highly correlated with TSS loads throughout the basin. Mercury 

concentrations are also highly correlated with arsenic concentrations at lower basin sites. 

According to loading estimates, the lower basin contributed approximately half of the mercury 

load calculated at Hat Slough. Low-level mercury concentrations are found in rainwater. The 

contributions of abandoned and inactive mining areas and ground water are not known. 

 
Stillaguamish Fecal and DO TMDL Submittal Report Page 95

Loading Capacity 

Fecal Coliform 

The fecal coliform bacteria (FC) loading capacities of waters within the Stillaguamish River 

basin and surrounding northern Port Susan are determined by protecting the most critical 

beneficial uses in those waters. The loading capacities are directly related to the bacteria 

distribution represented by the acceptable geometric mean and 90th percentile counts stated in the 

criteria. The following uses were considered the most critical uses for protection for various 

types of water of the basin. 

• Protecting recreational bathing provides the most restrictive criteria for the rivers and streams 

in the upper Stillaguamish basin. The loading capacities are represented as Class A or AA 

freshwater criteria. 

• Small freshwater streams discharging directly to Port Susan must meet the freshwater 

recreational bathing criteria, but they also must not result in violation of more restrictive 

Class A marine water criteria to protect recreation use or shellfish harvesting. The loading 

capacities for these sites are better represented by freshwater Class AA criteria to reduce 

actual mass loading of FC to Port Susan beaches during critical periods. 

• Port Susan sites must meet state Class A marine water criteria and Washington State 

Department of Health (DOH) commercial shellfish harvest criteria; the latter criteria are 

usually more stringent. The loading capacities of Port Susan sites are the FC population 

distribution characteristics compared to criteria based on the 30-sample DOH method. 

Seasonal analysis of data ensured that the loading capacities at each site are focused on critical 

FC loading and transport mechanisms. The loading capacity of each site was evaluated by using 

the statistical analyses described earlier. The 90th percentile was the most restrictive statistic at 

all sites not meeting criteria. Using the Statistical Rollback Method described earlier, FC 

geometric mean targets were calculated for sites not meeting the FC criteria. In theory, if the 

geometric mean target is met, then only 10% of a sample set should exceed the applicable 

FC criterion, e.g., 200 cfu/100 mL for Class A freshwater, or 43 MPN/100 mL for Class A 

marine water. 

Only six of 22 freshwater sites currently meet their loading capacities and both parts of the 

FC criteria under all conditions examined and for the most stable period of record (Table 26). 

All are located in the upper basin, and are highlighted in the table. The status of some sites is 

different from what was in Table 17 because of critical condition factors. 

The Stillaguamish River at Interstate 5, and the South Fork and the North Fork Stillaguamish 

River at Twin Rivers, met FC criteria on the first round of statistical analyses. However, all 

three sites showed signs of excessive FC loading from unidentified sources during storm events 

in 2001-2002. The lower reaches of the two forks could be responding to increased development 

near Arlington. The QUAL2Kw model simulations, storm-event data, and synoptic survey data 

also suggest there are FC loads from unidentified sources along reaches between Arlington and 
Page 96 Stillaguamish Fecal and DO TMDL Submittal Report

Port Susan. These could be from agricultural or residential uses adjacent to the river or along 

small drainages leading to the river. Detailed attention to land uses and BMPs in effect along 

this stretch of the river is required to develop an effective source reduction strategy. 

Table 26. Fecal coliform statistical summaries for freshwater monitoring sites along the mainstem 

Stillaguamish River and major forks and tributaries. Geometric mean and 90th 

percentile counts are cfu/100 mL. 

Site WQ 

Class* 

Number 

of Data 

Period of 

Record 

Critical 

Period 

Geometric 

Mean 

90th

 percentile 

Target 

Capacity 

Geometric 

Mean 

Hat Slough at Marine Drive FW – A 46 1998 - 2002 Jun - Dec 56 313 36 

Stillaguamish River at I-5 FW – A 21 2000 - 2002 Jun - Nov 54 417 26 

Stillaguamish below Arlington FW – A 25 1996 - 2002 May - Nov 52 357 29 

Stillaguamish above Arlington FW – A 54 1994 - 2002 May - Nov 50 260 39 

SF Stillaguamish at Arlington FW – A 17 2001 - 2002 43 216 40 

SF Stillaguamish at Granite Falls FW – AA 25 1996 - 2002 Jun - Sep 10 62 - 

NF Stillaguamish at Twin Rivers FW – A 9 2000 – 2001 32 232 28 

NF Stillaguamish at Cicero FW – A 31 1996 - 2002 Jul - Nov 14 177 - 

NF Stillaguamish at Whitman Br. FW – A 41 1997 - 2002 18 92 - 

NF Stillaguamish at C-Post Br. FW – A 28 1997 - 2002 9 69 - 

NF Stillaguamish near Darrington FW – A 34 1992 - 2002 Jun - Sep 14 96 - 

Glade Bekken FW – A 27 1999 - 2001 May - Nov 225 2,450 18 

Pilchuck Creek FW – A 65 1996 - 2001 May - Dec 51 272 38 

Portage Creek at 212th FW – A 126 1994 - 2001 147 1,170 25 

Portage Creek at 43rd FW – A 90 1994 - 2001 146 650 45 

Fish Creek FW – A 29 1997 - 2002 Dec - Jun 169 1,070 32 

March Creek FW – A 7 2000 - 2001 475 8,760 10 

Armstrong Creek at Mouth FW – A 19 1997 - 2001 60 280 43 

Armstrong Creek below Hatchery FW – A 37 1996 - 2002 67 583 23 

Kackman Creek at 252nd FW – A 20 1998 - 2002 104 630 33 

Harvey Creek at Grandview Road FW – A 22 1996 - 2002 Mar - Sep 158 830 38 

Jim Creek at Jordan Road FW – A 28 1996 - 2002 55 320 34 

Jim Creek at Whites Road FW – A 18 1998 - 2002 22 75 - 

* FW – A = Freshwater Class A; FW – AA = Freshwater Class AA 

Bolded names meet fecal coliform loading capacity by meeting state criteria. 

The Old Stillaguamish River Channel that splits from the mainstem before Hat Slough will be 

the subject of a more comprehensive TMDL evaluation in the future. However, none of the data 

from the nine tributary monitoring sites in this part of the basin met FC criteria, so preliminary 

FC loading capacities with target criteria were calculated (Table 27). Freshwater Class A FC 

criteria were used to calculate the loading capacities in all cases, since none of the sites directly 

discharge to beaches where shellfish harvesting or beach recreation occurs. Several of the sites 

had limited data and will need further monitoring to better characterize their current 

FC loading. At several of these sites, the target geometric mean counts required to meet the 

loading capacities are quite low because FC counts were the highest observed in the basin.
Stillaguamish Fecal and DO TMDL Submittal Report Page 97

Table 27. Fecal coliform critical condition summaries for tributaries to the Old Stillaguamish Channel near 

Stanwood. Geometric mean and 90th percentile counts are cfu/100 mL. 

Site WQ 

Class* 

Number 

of Data 

Period of 

Record 

Geometric 

Mean 

90th

percentile 

Target 

Capacity 

Geometric 

Mean 

Douglas Slough FW – A 70 1999 - 2002 40 620 13 

Irvine Slough FW – A 13 2000 - 2001 730 16,500 7 

Jorgenson Slough FW – A 31 1994 - 2001 320 1,580 42 

Church Creek at Park FW – A 97 1994 - 2001 147 770 38 

Miller Creek at Miller Road FW – A 21 2000 - 2002 311 2,350 28 

Twin City Foods Drain #1 FW – A 17 2001 406 3,550 24 

Twin City Foods Drain #2 FW – A 5 2001 285 23,100 3 

Twin City Foods Drain #3 FW – A 4 2001 1180 9,550 24 

Twin City Foods Drain #5 FW – A 6 2001 545 4,743 22 

 * FW – A = Freshwater Class A 

The several small freshwater tributaries discharging directly to Port Susan require more stringent 

criteria than Class A because their influence on the bacteriological quality of local recreational 

shellfish beds needs to be minimized. Therefore, their FC loading capacities should be Class 

AA: a geometric mean of 50 cfu/100 mL, and a 90th percentile count of less than 100 cfu/100 

mL (Table 28). The following three tributaries are recommended to be given targets to comply 

with a loading capacity based on Class AA freshwater criteria: Unnamed Creek #0456, Lake 

Martha Creek, and Warm Beach Dike Pond. Loading capacities for the two sites upstream of the 

Warm Beach Dike Pond – the Agricultural Drain and Warm Beach Creek – were calculated 

using Class AA criteria as well. 

Table 28. Fecal coliform critical condition summary for West Pass, South Pass, and small tributaries to 

Port Susan. Geometric mean and 90th percentile counts are cfu/100 mL. 

Site WQ 

Class* 

Number 

of Data 

Period of 

Record 

Critical 

Period 

Geometric 

Mean 

90th 

percentile 

Target 

Capacity 

Geometric 

Mean 

West Pass of Old Stillaguamish MW - A 17 2000 - 2001 85 1,250 3 

South Pass of Old Stillaguamish MW - A 26 2000 - 2001 42 150 11 

Twin City Foods Drain #4 FW - A 9 2001 149 1,670 18 

Warm Beach Creek above WWTP FW - AA 10 2001 - 2002 Jun - Nov 253 543 47 

Agricultural Drain to Warm Beach FW - AA 12 2001 - 2002 May - Nov 120 900 13 

Warm Beach Dike Pond FW - AA 12 2001 - 2002 May - Nov 172 1,300 14 

Warm Beach Slough MW - A 75 1998 - 2002 29 118 10 

Lake Martha Creek FW - AA 58 1996 - 2002 May - Oct 288 1,220 23 

Unnamed Creek # 0456 FW - AA 7 2001 350 3,600 11 

* MW - A = Marine Water Class A; FW - A = Freshwater Class A; FW - AA = Freshwater Class AA; 

The critical period for FC counts in Hat Slough at Marine Drive occurred from June through 

December (Table 26). The data collected by Ecology and Snohomish County at the Marine 

Drive site consistently exhibited freshwater conditions. The target loading capacity is based on 

Class A freshwater criteria. South Pass is another FC loading source to northern Port Susan from 

the Stillaguamish basin. It usually qualified as a marine site based on salinity, even though the 

highest FC counts were recorded during low salinity storm flows. The FC target capacity was 

set to meet the Class A marine water standards (Table 28). West Pass to Skagit Bay was treated 

in the same manner. 
Page 98 Stillaguamish Fecal and DO TMDL Submittal Report

The current upstream cumulative FC loads to Hat Slough were estimated and compared to 

estimated FC loads if the TMDL targets in Table 26 were met. The estimates were based on 

average daily loads derived from critical seasonal flows and the current and target geometric 

mean statistics. A natural die-off factor was not included in the calculations. The estimates 

suggest that if the targets are attained, the FC loads at Marine Drive will be reduced by 75%, 

quite adequate for meeting the 36% reduction required to meet Class A criteria at that site. The 

analysis also suggests that meeting the targets for the North and South forks, and mainstem 

targets below Arlington and at the Interstate 5 bridge, will be essential to reduce the FC loads by 

75%. The cumulative tributary FC load reductions will account for 20% of the overall load 

reduction. The other 55% will be from other reductions along the mainstem. 

Another simple estimate was made of the average daily FC loads to Port Susan for the months of 

June through December (Table 29). Hat Slough, South Pass, Warm Beach drainages, and 

wildlife sources were included in the estimate to consider a rough order of magnitude 

comparison between sources. The estimates of the wildlife loads have a large margin of error 

but demonstrate their potential importance as a background source. The estimates suggest an 

overall FC load reduction to Port Susan of 37%, and a 77% reduction from freshwater sources. 

Table 29. Estimated average daily fecal coliform loads to Port Susan from various sources for the months 

of June through December. Load estimates are shown for 2000 – 2002, current period, and for a time in 

the future when fecal coliform TMDL targets are met. 

Current 

Loading 

(cfu/day) 

Post-TMDL 

Loading 

(cfu/day) 

Hat Slough 12 x 1012 2.9 x 1012

South Pass 1 x 1012 0.2 x 1012

Warm Beach 

Drainages 0.2 x 1012 0.01 x 1012

Birds 5.2 x 1012 5.2 x 1012

Seals 8.5 x 1012 8.5 x 1012

Total 27 x 1012 17 x 1012

cfu = coliform-forming units per day. 

Data collected by the Stillaguamish Tribe in Hat Slough at the boat launch approximately 

0.5 kilometers downstream from Marine Drive yielded a 30-day sample geometric mean of 

15 MPN/100 mL (Table 30). Farther downstream were the South and West branches with 

geometric mean densities higher than in Hat Slough. The sites on the two branches were given 

target capacity geometric mean FC densities based on the DOH 30-sample criteria to reduce 

loading between the Stillaguamish Tribe Hat Slough site and Port Susan. 

Some Port Susan sites were not meeting DOH 30-sample criteria for commercial harvest areas. 

The statistics for the last 30 samples are shown in Table 30. They are not significantly different 

from the statistics derived from the whole set of samples collected by the Stillaguamish Tribe 

since 1998. The loading capacities for Port Susan sites were calculated by using the Statistical 

Rollback Method so that the criteria of a 90th percentile of 43 MPN/100 mL and a geometric 

mean of 14 MPN/100 mL will be met: 
Stillaguamish Fecal and DO TMDL Submittal Report Page 99

• The loading capacities represented by the geometric mean targets are generally around 10 

MPN/100 mL to meet the 90th percentile criterion of 43 MPN/100 mL. 

• Kayak Point, Warm Beach Point, and North Port Susan meet criteria. 

• The number of samples for PS-5 through PS-9 and Juniper Beach are inadequate for a 30-

sample calculation. 

• The FC reductions required for Port Susan sites vary from 2% to 60%. 

Table 30. Fecal coliform target geometric means calculated from statistics derived for 30 consecutive 

samples collected by the Stillaguamish Tribe prior to June 27, 2002 at 16 sites in Port Susan and the 

Stillaguamish River estuary. Geometric mean and 90th percentile counts are MPN/100 mL. 

Site Name 

Hat 

Slough 

West 

Branch 

South 

Branch 

SB 

Pilings 

WB 

Slough PS-2 PS-7** PS-6** 

Site Number 120 121 122 123 127 128 139 138 

Geometric Mean 15 27 24 12 28 21 32 19 

90th percentile 64 98 102 44 100 107 125 117 

Target Capacity 

Geometric Mean NR* 12 11 11 12 8 11 7 

* NR = none required 

** Less than 30 samples available to calculate statistics. 

SB = South Branch; WB = Warm Beach; PS = Port Susan 

A 77 percent reduction in freshwater FC loads to Port Susan is estimated if FC loading capacities 

are met in the Stillaguamish River, its tributaries, and the Warm Beach drainages. The 

freshwater FC loads are the likely cause of criteria violations in Port Susan since seals and birds 

are present in winter and spring when criteria in the bay are often met. Estimated FC reductions 

required for sites in Hat Slough, the Stillaguamish River estuary, and Port Susan are close to 60 

percent in Hat Slough and are as low as 2 percent in the estuary. The level of freshwater FC load 

reduction should allow sites in Port Susan to meet water quality criteria for shellfish harvesting. 

Site Name PS-3 PS-5** PS-8** PS-4 PS-9** 

WB 

Point 

Kayak 

Point 

NP 

Susan 

Juniper 

Beach** 

Site Number 129 137 140 130 148 124 125 126 - 

Geometric Mean 14 21 15 5.7 3.9 6.1 4.2 3.3 15 

90th percentile 74 148 119 27 13 31 20 12 65 

Target Capacity 

Geometric Mean 8 6 6 NR NR NR NR NR 10 
Page 100 Stillaguamish Fecal and DO TMDL Submittal Report

Dissolved Oxygen 

The dissolved oxygen (DO) loading capacities of waters within the Stillaguamish River basin are 

determined by protecting the most critical beneficial uses in those waters. The loading capacities 

are directly related to the minimum DO concentration stated in the criteria, or to natural 

conditions as defined in Chapter 173-201A-070 WAC. Salmonid spawning is considered the 

most critical beneficial use in the Stillaguamish River basin requiring adequate oxygen 

concentrations. Salmonid rearing and migration, and life support for other fish and aquatic 

communities, require less stringent oxygen concentrations. 

Twelve reaches in the basin were identified as not meeting the Class A water quality criterion of 

8 mg/L. Two reaches are on the mainstem Stillaguamish River, and the other ten are on 

tributaries to the Stillaguamish River or to Port Susan. One reach on the 1998 303(d) list – 

South Fork Stillaguamish at Granite Falls (Class AA at 9.5 mg/L) was found not to have DO 

impairment. This evaluation recommends this water body segment be taken off the 303(d) list. 

These three sites will be required to meet the minimum Class A DO criteria of 8 mg/L. 

• The Stillaguamish River above Hat Slough has experienced low DO in the past because 

deoxygenated water from the Old Stillaguamish Channel has flowed back into the main river 

channel. A tide gate installed in 2003 should prevent the problem from occurring in the 

future and keep minimum freshwater DO concentrations above 8 mg/L. Incoming marine 

water may occasionally lower DO concentrations in Hat Slough to 6.5 mg/L. 

• Warm Beach Creek above the WWTP outfall has several likely upstream sources of BOD, 

ammonia, and oxygen-demand. Although insufficient flow volumes may be a significant 

factor for making DO measurements in the summer, any flowing water in the creek should be 

free of oxygen-demanding contaminants so that the 8.0 mg/L Class A criterion will be met. 

• DO concentrations measured at Pilchuck Creek at Jackson Gulch Road have been 

infrequently below 8 mg/L. Removing or reducing documented nonpoint and stormwater 

sources upstream of the site should bring DO back into compliance. 

Two ‘natural condition’ issues concerning the DO results have made it difficult to evaluate 

minimum potential concentrations at the other nine sites: 

• The floodplain reaches of some tributaries to the lower Stillaguamish River and ditches 

through diked lands have naturally low DO from surrounding wetlands and valley 

groundwater inputs. Several of the reaches also exhibit low pH (near 6.5) and cool water 

temperatures that also indicate wetland or groundwater inputs. However, nonpoint sources 

also may contribute to some of the low DO conditions in these tributaries. Fecal coliform 

criteria are not met in these reaches, but low DO concentrations and elevated FC counts are 

not strongly correlated at any of the monitoring sites. 

• The seasonally low DO conditions in the Stillaguamish River between Arlington and I-5 

appear to be dominated by some sort of benthic demand. QUAL2Kw model results suggest 

that areas of hyporheic exchange are causing DO depressions in one or two pools in the 

reach. These processes are difficult to model, and the DO loss due to natural conditions may 

be more significant than that caused by upstream source nutrient and BOD inputs. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 101

At most of these sites, an estimate of the best potential minimum DO concentration is necessary 

because DO is suspected of being naturally lower than the Class A criterion of 8 mg/L. The 

estimated minimum concentrations are listed in Table 31. The concentrations were based on best 

professional judgment after considering natural and anthropogenic inputs. More detailed data 

and the removal of nonpoint sources of pollutants will be required before the natural DO minima 

for these systems can be fully determined. 

Table 31. Dissolved oxygen minimum concentrations estimated for reaches in the Stillaguamish River 

basin based on considerations of local natural and pollutant sources. The load capacities as BOD5 are 

estimated from reductions of nonpoint sources. 

Site 

Waterbody 

ID 

Number 

Concentration 

Range 

(mg/L) 

Potential 

Minimum DO 

at Critical 

Period (mg/L) 

Load 

Capacity 

BOD5

(lbs/day) 

Twin City Foods Drain #4 - 1.2 – 18.8 6.5 (a) 

Warm Beach Creek above WWTP Outfall SH96KX 3.8 – 8.4 8 20 

Pasture Drain to Pump Pond SH96KX 4.1 – 12.0 6.5 10 

Pond or Discharge to Warm Beach Slough SH96KX 3.0 – 9.1 6.5 30 

Pilchuck Creek at Jackson Gulch Road VJ74AO 7.6 – 13.6 8 890 

Portage Creek at 212th OT80TY 5.1 – 12.2 6.5 300 

Portage Creek at 15th OT80TY 3.7 – 7.2 6.5 280 

Portage Creek at 43rd OT80TY 6.4 – 11.4 7 250 

March Creek at 220th NE WI88QF 4.8 – 8.0 6.5 30 (b) 

Kackman Creek at 252nd XB43NX 6.6 – 9.0 7 10 

Stillaguamish River below Arlington QE93BW 7.3 – 14.1 7 (c) 

Stillaguamish River above Hat Slough QE93BW 5.7 – 13.2 8 (d) 

(a) Twin City Foods Drain #4 could not be estimated because the drainage area was not known, and water in the 

drain was never running 

(b) A 75% reduction in BOD5 for March Creek was estimated rather than using the 98% reduction required for fecal 

coliform to meet standards 

(c) Analysis using QUAL2Kw modeling (pp. 100 – 103) indicates data are not sufficient to determine load capacity 

(d) Tidegate at upper end Old Stilly Channel expected to reduce input of low-Dissolved Oxygen water into 

mainstem (Hat Slough). 

An estimate of oxygen demand from anthropogenic sources is required to estimate the best 

potential minimum DO concentration. In this analysis, the presence of elevated fecal coliform 

bacteria and nutrients was assumed to come from the same anthropogenic sources as excess 

oxygen demand. All of the tributaries in Table 31 require fecal coliform reductions. These 

reductions were used as relative gages of BOD reduction. 

The Simple Method model (Stormwater Center, 2004) that calculates runoff pollutant loads from 

various land uses was used to estimate current BOD5 loading. The model estimates of current 

loads were checked against loads generated from mean flow statistics and the few available 

BOD5 sample data, and were found to be similar in magnitude. The loading capacities were 

estimated by applying reductions based on the fecal coliform loading capacities (Tables 26, 27, 

28, and 30). The loading capacities yield average BOD5 concentrations around 1 mg/L 

compared to 1.5 to 3 mg/L BOD5 estimated for current conditions. 
Page 102 Stillaguamish Fecal and DO TMDL Submittal Report

The estimated potential minimum DO concentrations in Table 31 are no lower than the Class B 

6.5 mg/L minimum DO concentration in Washington State Chapter 173-201A WAC to protect 

fish and aquatic life, and salmonid life stages other than embryo and larval development. 

Portage Creek, March Creek, and Kackman Creek have been identified as coho salmon or winter 

steelhead habitat (WCC, 1999). All of the monitoring sites on these creeks are located in large, 

slow pools or in grass-choked channels that would not be considered good spawning habitat. 

The estimated DO concentrations may be adequate for salmon egg development and for fry 

survival and growth. The adequacy of DO concentrations for egg development and fry viability 

is dependent on sediment porosity and the velocity of the water reaching the egg or fry (Warren, 

1971). The Class A criterion of 8 mg/L will provide more than adequate DO through coho and 

steelhead redds in most, but not all, cases,. However, egg and fry can survive and thrive at lower 

water column DO concentrations (greater than 5 mg/L) if redds are placed in porous gravels and 

water velocities that allow good circulation of DO and nutrients (Warren, 1971). 

Coho spawning and egg incubation occurs from October through May, so the most serious 

periods of minimum DO concentrations may be avoided. Winter steelhead spawning and egg 

incubation in Portage Creek and Kackman Creek span November to July, so the late incubation 

period would be most critical for attaining adequate DO in spawning areas of these streams. 

Investigating the quality and location of spawning areas in these creeks was beyond the scope of 

this TMDL evaluation. The relationships between DO concentrations and salmon egg and fry 

survival at this level of detail have not been made. More complete assessments will be required 

to ensure that DO is not a habitat-limiting factor in spawning areas. 

An attempt was made to determine the loading capacities of phosphorus, BOD, ammonia, and 

nitrogen for the Stillaguamish River between Arlington and Interstate 5. The QUAL2Kw model 

(Chapra and Pelletier, 2003) was used to simulate the effects of carbon, nitrogen, and phosphorus 

loads on DO under low-flow critical conditions (Table 20). Heterotrophic bacteria and 

periphyton growth, and hyporheic exchange functions used to simulate conditions recorded in 

August 1997 and October 2001, were included. The input values and coefficients used in the 

model are available in Appendix C. 

The nutrient and BOD loads from Arlington WWTP and nonpoint sources were varied 

successively to compare their effects on DO changes in downstream reaches. These were 

compared to the minimum DO concentrations under simulated natural conditions (no 

anthropogenic inputs). Headwater nutrient loads were also varied in the set of simulations. The 

results of these simulations are summarized in Table 32. An example of two DO profiles is 

shown in Figure 25. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 103

Table 32. Summary of QUAL2Kw simulations of Arlington WWTP input and Stillaguamish River minimum 

dissolved oxygen (DO) responses during critical low-flow conditions. 

Arlington WWTP effluent Downstream 

Response 

BOD5 SRP NH3 NO3 Minimum DO Model Simulations 

mg/L mg/L mg/L mg/L mg/L 

1 1997 Arlington Loading (0.024 cms) 10.8 2.6 0.8 9.7 6.5 

2 2001 Arlington Loading (0.052 cms) 8 3.5 0.6 2 6.4 

3 Arlington Phase I permit (0.088 cms) 45 3.0 1.0 2 6.3 

4 Arlington Phase II permit (0.131 cms) 45 3.0 1.0 2 6.2 

5 Arlington Phase I - BOD modified 10 3.0 1.0 2 6.4 

6 Option 5 + SRP modified 10 1.0 1.0 2 6.4 

7 Arlington Phase I – no SRP 10 0 1.0 2 6.5 

8 No Arlington WWTP but NPS present 0 0 0 0 6.6 

9 Arlington Phase I but no NPS present 10 1.0 1.0 2 6.7 

10 No Arlington WWTP or direct NPS 0 0 0 0 6.9 

11 10 + Headwaters nutrient reductions * 0 0 0 0 7.2 

12 11 + Arlington Phase I modified 10 1.0 1.0 2 7.0 

13 12 + NPS present 10 1.0 1.0 2 6.7 

* Nutrients reduced to North Cascades Ecoregion reference concentrations (Table 8) 

 NPS - Unidentified nonpoint source loads 

Figure 25. Two QUAL2Kw model simulations showing the range of diel dissolved oxygen 

concentrations in the Stillaguamish River from the confluence of the forks to Port Susan. 

Simulation 5 and 7 conditions are described in 

Table 32. 

5.0

6.0

7.0

8.0

9.0

10.0

11.0

12.0

28.5 26.5 24.5 22.5 20.5 18.5 16.5 14.5 12.5 10.5 8.5 6.5 4.5 2.5

River Kilometer

Dissolved Oxygen (mg/L)

Simulation 5

Simulation 7

Confluence Interstate 5 Old Channel

River Flow Direction
Page 104 Stillaguamish Fecal and DO TMDL Submittal Report

In all simulations, the minimum DO concentration located around RKM 20 was far lower than 

any DO observed in the 1997 and 2001 field surveys. For example, the 6.5 mg/L DO minimum 

in the August 1997 loading scenario (Simulation 1) is nearly 1 mg/L lower than what was 

observed in the field at that time. Slightly higher water temperatures and headwater 

concentrations of nutrients required for the critical conditions settings may have caused the 

difference. However, even natural background (Simulations 10 and 11) results, with 

anthropogenic (point and nonpoint) sources of phosphorus and carbon absent as natural 

conditions, were 0.8 and 1.2 mg/L below the Class A DO criterion. The scenarios with 

anthropogenic sources (Simulations 1- 9, 12, 13) result in DO concentrations 0.2 – 0.7 mg/L 

lower than the natural background scenarios. 

The simulation results suggest that the instream processes, represented in QUAL2Kw by 

periphyton biomass growth and the heterotrophic bacteria growth in the hyporheic zone, may be 

the dominant factors controlling minimum DO concentrations during low-flow conditions. How 

periphyton and heterotrophic bacteria biomass are affected by the combination of carbon, 

ammonia, nitrogen, and phosphorus loads cannot be confidently determined at this time. The 

instream processes are too biologically and physically dynamic. 

Extrapolating a single model calibration of these processes to critical conditions and calculating 

loading capacities for BOD, phosphorus, and nitrogen is not technically defensible at this time. 

For example, the DO results in the model are very sensitive to both the initial biomass and 

growth rates of periphyton and heterotrophic bacteria, and their placement along the reach. 

Since the model is only quasi-dynamic, the initial periphyton biomass had to be set near the 

value measured when the greatest DO range was measured, and the growth rates had to be 

calibrated to field data. 

Heterotrophic bacteria initial biomass and rate values were added by trial-and-error calibration. 

Biggs (2000) showed that the number of days for biomass accrual had more of an effect than 

nutrient concentrations on maximum chlorophyll a biomass, but both were important factors. 

The same is possibly true for the heterotrophic communities as well. Since changes in the 

accumulation rates of periphyton biomass and heterotrophic bacteria biomass have not been 

quantified for the Stillaguamish system, the initial biomass of these populations at the onset of 

critical conditions is uncertain. 

As stated earlier, when the Washington State DO standard cannot be met under natural 

conditions, the natural condition becomes the DO criterion (Chapter 173-201A-070 WAC). It is 

Ecology’s policy that effluents cannot cause more than a 0.2 mg/L loss of DO in areas where 

natural conditions are lower than standards (TMDL Workgroup, 1996). The results in Table 32 

suggest that Arlington WWTP effluent and nonpoint sources in the reach may reduce DO by 

0.2 mg/L or greater. The survey data and research literature suggest that carbon and phosphorus 

loading to the reach stimulates periphyton growth. However, the margin of error in the 

simulations is too great to determine if 0.2 mg/L is a significant additional loss compared to 

background because of the complex biological processes in the reach. 

The QUAL2Kw model predicted a potential minimum DO concentration at RKM 21.7 

(RM 13.5) in the Stillaguamish River between Arlington and the Interstate 5 bridge of 6.9 to 

7.2 mg/L under critical conditions (Simulations 10 and 11, Table 32). Therefore, a minimum 
Stillaguamish Fecal and DO TMDL Submittal Report Page 105

DO concentration of 7 mg/L should be attainable under critical conditions if upstream, nonpoint 

source, and point source nutrient inputs are managed and controlled. DO concentrations below 

7.3 mg/L have not been detected outside of the single pool area, so the spatial extent of the 

7 mg/L minimum would be very limited. As described previously in the tributary DO 

discussion, salmon spawning and rearing area and other beneficial uses in the reach should be 

protected at this minimum DO target. 

pH 

As with dissolved oxygen, the contaminant loading capacities for water bodies with pH criteria 

violations vary by cause. The Stillaguamish basin water bodies with pH values higher than the 

8.5 criterion probably have excessive aquatic biomass with high productivity. Nutrient loading 

is controlled to reduce biomass in these cases and to lower diel pH maxima. In water bodies 

with pH values lower than the 6.5 criterion, the causes could be from several natural or 

anthropogenic causes. Anthropogenic loading of low pH water or organic contaminants that 

increase decomposition processes needs to be reduced to increase pH to natural conditions. 

The areas in the Stillaguamish basin with low pH criterion violations are observed either 

seasonally or during storm events. The ability of these water bodies to meet the pH criterion 

once anthropogenic sources of oxygen demand or low pH water are reduced is not known. The 

loading capacities cannot be calculated. The following sites should be reassessed to determine 

natural seasonal or event-based pH conditions once the anthropogenic sources of oxygendemand or low pH stormwater are reduced or eliminated as fecal coliform and dissolved oxygen 

loading capacities are met. 

• Stillaguamish River above Arlington at the confluence of the North and South forks 

• Pilchuck Creek 

• Kackman Creek 

• March Creek 

The North Fork Stillaguamish River at Whitman bridge to Cicero bridge (NFRKM 28.3 to 

NFRKM 15.2) was the only location where seasonal episodes of pH maxima over criteria are 

recorded. The TMDL data collected did not specifically find pH values over the 8.5 s.u. 

criterion, but historical data at Cicero and frequency of data near 8.5 s.u. are strong indications 

that this does occur. Nutrients increases since 1995 are not apparent from data in this reach, but 

some increases may have occurred since the 1980s. 

The nutrient loading capacity for the North Fork Stillaguamish was not explored in depth 

because the problem in the area was not previously identified on the 303(d) list. However, trend 

analyses on data collected at Ecology 05B070, North Fork Stillaguamish at Cicero, suggests a 

significant increasing trend in total phosphorus loads at the site since 1980 (Figure 26). 

According to Ecology monthly monitoring data, phosphorus loads have not increased upstream 

at the site near Darrington (05B110), and pH there has been well within criteria. Sources of 

phosphorus between 05B110 (RKMNF 48.3) and Cicero bridge (RKMNF 15.2), starting above 

Whitman bridge (RKMNF 28.3), have not been specifically identified. Potential nonpoint 

sources of phosphorus include residential, highway, and agricultural runoff. 
Page 106 Stillaguamish Fecal and DO TMDL Submittal Report Total Phosphorus Load (lbs/day) 

YEAR

 1

 2

10

20

 100

 200

1000

2000

 10000

 20000

100000

200000

 1000000

ALL SEASONS 

Seasonal Sen Slope

Stand/Crit

79 85 90 95 00 02

SEASONAL KENDALL (SKWOC)

Slope = 1.44164 

Signif 90%

2xP = 0.0915

Figure 26. Total phosphorus load trend in monthly data collected by Ecology at the North Fork 

Stillaguamish River (Station 05B070) from 1979 to 2002. 

Reducing the total phosphorus load may improve the July through September low-flow pH 

conditions by decreasing the biomass responsible for the elevated pH values. Bringing the 

median seasonal total phosphorus concentration to 0.01 mg/L will be equal to the 1987 to 1995 

seasonal average. The 0.01 mg/L total phosphorus value is between the Puget Sound and 

North Cascades summer reference values of 0.017 and 0.0025 mg/L, respectively (EPA, 2000). 

This represents a seasonal total phosphorus loading capacity of 21 lbs/day. 

Arsenic and Mercury 

Arsenic is available from natural geologic sources in the basin, and no loading capacity 

calculation is necessary or possible. Arsenic concentrations are consistently above the 0.14 ug/L 

EPA human-health criteria based on a 1:1,000,000 carcinogenic risk. Arsenic concentrations in 

the Stillaguamish River are far below aquatic toxicity criteria. No evidence of anthropogenic 

sources of arsenic was uncovered in the data analysis. This TMDL evaluation recommends that 

arsenic be removed from the 303(d) list for the Stillaguamish River. 

Mercury is also available from natural geologic sources in the Stillaguamish River basin. 

Mercury concentrations throughout the basin may periodically exceed the 0.012 ug/L chronic 

aquatic toxicity criterion. The mercury criterion is a four-day average concentration that is not to 
Stillaguamish Fecal and DO TMDL Submittal Report Page 107

be exceeded more than once every three years. Samples were not collected over four-day 

periods to measure exact compliance with the criterion. 

Mercury concentrations collected near the mouths of the North and South forks, and two sites in 

the mainstem Stillaguamish River, were correlated with total suspended solids (TSS) 

concentrations. Reducing TSS, especially TSS mobilized during storm events, would reduce 

mercury transport and availability. The correlation between TSS and mercury concentrations is 

shown in Figure 27. 

y = 0.0011x0.5704

R2 = 0.8269

0.001

0.01

0.1

1

1 10 100 1000

TSS (mg/L)

Hg (ug/L)

Chronic toxicity criterion

 

Figure 27. Relationship between total suspended solids (TSS) and mercury (Hg) in samples 

collected by Ecology from two sites on the Stillaguamish River, two sites on the lower North Fork 

Stillaguamish River, and at the mouth of the South Fork Stillaguamish River. The EPA 0.012 

ug/L chronic aquatic toxicity criterion is also shown. 

A target TSS concentration to limit mercury concentrations greater than the aquatic toxicity 

criterion could be based on the regression equation relating TSS in mg/L to mercury in ug/L: 

 Mercury = 0.0011 x TSS 0.5704 

An average four-day TSS concentration of 65 mg/L would limit the mercury concentration to 

0.012 ug/L. The TSS concentrations are not well correlated with discharge at any of the sites. 

Sudden increases in runoff generally create increases in TSS. The TSS concentrations in the 

lower portion of the two forks and in the mainstem Stillaguamish River often peak much greater 

than 65 mg/L during storm events, but usually drop rapidly over the next couple of days. 
Page 108 Stillaguamish Fecal and DO TMDL Submittal Report
Stillaguamish Fecal and DO TMDL Submittal Report Page 109

Wasteload and Load Allocations 

It is a task of the total maximum daily load evaluation to recommend wasteload allocations and 

load allocations. The wasteload allocations are derived for point sources with NPDES or state 

waste permits, and load allocations are derived for nonpoint sources. Together the allocations 

must meet the load capacity for each water body. 

Fecal Coliform 

The TMDL evaluation has demonstrated that fecal coliform (FC) bacteria criteria violations are 

prevalent throughout the lower Stillaguamish River basin, especially during storm events. The 

water bodies in Table 33 were on the 1998 Section 303(d) list for impairments due to excessive 

FC bacteria. All 12 water bodies still require FC reductions to meet criteria. The table lists the 

total FC reduction required for each water body to meet the appropriate FC criteria. The FC 

bacteria reductions are based on the roll-back determinations in Tables 26 - 29. Most of the 

tributaries require more than a 70 percent FC reduction to meet criteria. Mainstem and major 

branches require less than a 70 percent FC reductions. 

 

Table 33. Stillaguamish River basin and Port Susan tributaries listed in Section 303(d) in 1998. Fecal 

coliform reductions necessary to meet Washington State water quality criteria are shown. The status of 

the water body on the 1996 303(d) is also shown. 

Old WBID New WBID Name 

Current Load 

(cfu/day) 

Fecal 

Coliform 

Reductions 

1996 

303(d) 

WA-05-1016 QJ28UC Fish Creek 7.4 x 1010 81% Yes 

 HD76OJ Harvey Creek 2.33 x 1010 76% No 

 JU33JU Jim Creek at Mouth 4.00 x 1011 38% No 

WA-05-1012 GH05SX Jorgenson Slough 

(Church Creek) 

** 87% Yes 

 IJ55EP Lake Martha Creek 6.38 x 1010 92% No 

WA-PS-0020 390KRD Port Susan ** 61% Yes 

WA-05-1015 OT80TY* Portage Creek at 212th

NE 

4.16 x 1011 83% Yes 

WA-05-1015 OT80TY Portage Creek at 43rd 3.69 x 1011 69% Yes 

WA-05-1010 QE93BW Stillaguamish River at I-5 6.27 x 1012 52% Yes 

WA-05-1010 ZO73WL Stillaguamish River at 

Marine Drive 

5.79 x 1012 36% No 

WA-05-1020 WO38NV N.F. Stillaguamish River 

(at mouth) 

1.95 x 1012 14% Yes 

WA-05-1050 SN06ZT S.F. Stillaguamish River 

(at mouth) 

2.24 x 1012 7% Yes 

 LU17DC Unnamed Creek #0456 5.17 x 1010 97% No 

* Includes the listings mistakenly assigned to QJ28UC, Fish Creek, and YF03BC, a branch of Portage Creek, 

but should have been entered as OT80TY, Portage Creek ** Insufficient flow measurement to calculate load. 
Page 110 Stillaguamish Fecal and DO TMDL Submittal Report

This TMDL evaluation identified 23 additional tributaries or tributary reaches, drains, and 

sloughs that do not meet the FC criteria. Water bodies in Table 34 were not on the 1998 Section 

303(d) list for FC bacteria, but require FC reductions to meet state criteria and fully support 

beneficial uses. Most of the water bodies in Table 34 require FC reductions greater than 70%. A 

few of the water bodies in Table 34 were on the 1998 303(d) list for dissolved oxygen, pH, or 

temperature. Others have been known to local groups as potential problems for several years, 

but have not been included in the 305(b) statewide assessment. 

Table 34. Additional Stillaguamish River basin and Port Susan tributaries not listed in 

Section 303(d) in 1998. Fecal coliform reductions necessary to meet Washington State water quality 

criteria are shown. 

 Name Water Quality 

Classification 

Current Load 

(cfu/day) 

Fecal Coliform 

Reductions

Glade Bekken FW - A 7.42 x 1010 92% 

Pilchuck Creek FW - A 4.89 x 1011 26% 

March Creek FW - A 9.35 x 1010 98% 

Armstrong Creek at Mouth FW - A 1.01 x 1011 29% 

Armstrong Creek below Hatchery FW - A * 66% 

Kackman Creek FW - A 1.79 x 1010 68% 

West Pass of Old Stillaguamish FW/MW - A 6.1 x 1010 97% 

South Pass of Old Stillaguamish FW/MW - A 2.45 x 1011 75% 

Douglas Slough FW/MW - A * 68% 

Irvine Slough FW/MW - A * 99% 

Church Creek at Park FW - A * 74% 

Miller Creek at Miller Road FW - A * 91% 

Twin City Foods Drain #1 FW/MW - A * 94% 

Twin City Foods Drain #2 FW/MW - A * 99% 

Twin City Foods Drain #3 FW/MW - A * 98% 

Twin City Foods Drain #4 FW/MW - A * 88% 

Twin City Foods Drain #5 FW/MW - A * 96% 

Warm Beach Creek above WWTP FW - AA 3.11 x 1010 81% 

Agricultural Drain to Warm Beach FW - AA 8.86 x 1009 89% 

Warm Beach Dike Pond FW - AA 4.23 x 1010 92% 

Warm Beach Slough MW - A * 64% 

* Insufficient flow measurements to quantify the load.

Ten of the water bodies in Table 34, and Jorgenson Slough (Church Creek) in Table 33, are 

tributaries to, or located in, the Old Stillaguamish Channel sub-basin. As stated earlier in this 

report, a more complete analysis of the Old Stillaguamish Channel will be conducted at a later 

date when the effects of the new tide gate and upgraded Stanwood Wastewater Treatment Plant 

(WWTP) can be evaluated. The FC load reductions for the 11 water bodies listed in the tables 

are accurate and can be considered general load allocations. Implementation of nonpoint source 

controls should not be delayed in these sub-basins. 

The major source of FC contamination in most of the water bodies in Tables 32 and 33 is 

nonpoint runoff from mixed land uses. The TMDL evaluation did not identify the FC load 

associated with specific properties or land uses for these water bodies. Therefore, most of the 

required reductions are load allocations to general nonpoint sources. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 111

However, the EPA now requires wasteload allocations for all NPDES stormwater permit holders 

(Wayland and Hanlon, 2002). Since Snohomish County and the Washington State Department 

of Transportation are Phase 1 Stormwater NPDES permit holders, most of the load reductions in 

Tables 32 and 33 require at least one WLA for stormwater. Arlington and Granite Falls Phase 2 

stormwater permit applicants are also jurisdictions that may require stormwater wasteload 

allocations for some water bodies in Tables 32 and 33. 

Wasteload allocation estimates for Snohomish County and the WSDOT in Table 35 are 

calculated on roadway areas, and Arlington wasteload allocations are estimated from all land 

uses within the city limits (see Analytical Framework). (Note that EPA guidance [Wayland and 

Hanlon, 2002] indicates that NPDES stormwater permits will address these wasteload allocations 

through Best Management Practices rather than through numeric effluent limits.)

 

Table 35. Fecal coliform (FC) wasteload allocations for stormwater discharge permit holders, Snohomish 

County and the Washington State Department of Transportation, as well as a 

 stormwater permit applicant, the city of Arlington. 

Water Body NPDES Permit Holder Estimated Portion 

of FC Load (%) 

Wasteload 

Allocations 

(cfu/day) 

Fish Creek Snohomish County 5% 5.35 x 108

Harvey Creek at Grandview Snohomish County 1.2% 6.59 x 107

Jim Creek at Mouth Snohomish County 1.6% 4.34 x 109

Portage Creek at 212th Snohomish County 

WSDOT 

2.9% 

1.8% 

1.92 x 109

1.18 x 109

Portage Creek at 43rd Arlington 39% 4.44 x 1010

Lake Martha Creek Snohomish County 8.8% -- 

Unnamed #0456 Snohomish County 6.9% -- 

Glade Bekken Snohomish County 6.5% 1.30 x 108

Pilchuck Creek Snohomish County 

WSDOT 

2.5% 

16.5% 

8.54 x 109

5.57 x 1010

March Creek Snohomish County 

WSDOT 

Arlington 

0.4% 

1.2% 

19% 

7.15 x 106 

2.42 x 107

3.71 x 108

Armstrong Creek at Mouth Snohomish County 

WSDOT 

2.3% 

1.2% 

1.63 x 109

8.04 x 108

Kackman Creek at 252nd Snohomish County 3.6% 1.71 x 108

Warm Beach Dike Pond Snohomish County 4.3% -- 

North Fork Stillaguamish at Mouth Snohomish County 

WSDOT 

2.1% 

1.5% 

3.0 x 1010

2.1 x 1010

South Fork Stillaguamish at Mouth Snohomish County 

Arlington 

2.9% 

5.6% 

6.07 x 1010

1.16 x 1011

The Arlington WWTP, Indian Ridge WWTP, and Warm Beach Conference Center WWTP 

discharge to water bodies requiring FC load reductions: Stillaguamish River above Arlington, 

Jim Creek, and Warm Beach Creek, respectively (Tables 32 and 33). The FC wasteload 

allocations for the treatment plants are based on calculations using upstream FC counts, the 

mixing zone characteristics at the outfall, and the FC loading capacity of the receiving water. 

The current NPDES permits for these facilities have FC limits (Appendix A), but because of the 

TMDL, some of the limits require modification. 
Page 112 Stillaguamish Fecal and DO TMDL Submittal Report

In most cases, the compliance point for FC is at the edge of the chronic mixing zone boundary 

(Bailey, 2002). Indian Ridge WWTP can meet the downstream FC target on Jim Creek under 

current permit limits of 100 cfu/100 mL (Table 36). However, since the FC water quality above 

the Arlington WWTP and Warm Beach Conference Center WWTP do not meet FC criteria in 

their respective receiving waters, the effluent from these facilities cannot increase the FC 

concentration or load. Therefore, adjustments to the FC limits in their NPDES permits are 

necessary (Table 36). These concentration limits must be met at the end of the outfall. 

 

Table 36. Recommended fecal coliform limits and wasteload allocations (WLA) for 

three wastewater treatment plants with NPDES permits. 

Current FC Permit Proposed Permit Facility Name cfu/100 mL cfu/100 mL WLA 

cfu/day 

Indian Ridge Corrections Center WWTP 100 100 8.0 x 108

Arlington WWTP 200 / 400 39 / 128 3.0 x 109

Warm Beach Conference Center WWTP* 200 / 400 47 / 100 1.3 x 108

Warm Beach Conference Center WWTP** - 11 / 26 3.1 x 107

* Assuming discharge to Warm Beach Creek at current maximum monthly flow of 0.075 MGD, 

 and the discharge is allowed under special considerations. 

** Assuming discharge to Hat Slough near the South Branch with maximum monthly flow of 

0.075 MGD. 

Warm Beach WWTP effluent quality has improved according to 2002 monitoring reports 

(Ecology, 2003a) and additional data from the facility manager (Wynn, 2002) for 2002. The 

Warm Beach WWTP facility has added a wetlands treatment system that should further reduce 

the effluent FC and the variability from this source. The outfall location for the improved 

facility has not yet been determined. If the outfall remains in Warm Beach Creek, the effluent 

would be required to meet the TMDL target concentrations at the end of the outfall because the 

channel is dry during some summer periods. Municipal effluent discharges under 0.5 million 

gallons per day (MGD) are allowed to intermittent low-land streams if the effluent quality can 

meet Class A water quality criteria (Bailey, 2002). It is uncertain how this applies to TMDL 

modified intermittent streams. If the Warm Beach WWTP outfall is moved to Hat Slough near 

South Branch, Table 36 shows the FC permit limits would be more restrictive than in Warm 

Beach Creek. This is because of the geometric mean target for the South Branch reach is 

11 cfu/100 mL (Table 30). 

Dissolved Oxygen 

Loading capacity analyses were conducted for nine reaches representing five tributaries in the 

Stillaguamish River basin (Table 31). Estimated potential minimum DO concentrations are 

shown in the table to acknowledge that in some cases, and at certain times, natural DO 

conditions may be below the 8 mg/L Class A criterion. Wasteload allocations for point sources 

with NPDES permits, and load allocations for nonpoint sources, were calculated for the five 

tributaries where appropriate (Table 37). (Note that EPA guidance [Wayland and Hanlon, 2002] 

indicates that NPDES stormwater permits will address these wasteload allocations through Best 

Management Practices rather than through numeric effluent limits.) 

 
Stillaguamish Fecal and DO TMDL Submittal Report Page 113

Snohomish County and the Washington State Department of Transportation (WSDOT) are 

Phase I Stormwater NPDES and State General Permit holders in the five tributaries. The city of 

Arlington is a Phase 2 Stormwater Permit applicant. The Simple Method Model (Stormwater 

Center, 2004) was used to estimate the BOD5 wasteload allocations for the permit holders, as it 

was for the fecal coliform stormwater permit wasteload allocations. 

Load allocations were estimated for background and nonpoint contributions of BOD5. 

Background loads were estimated by minimizing BOD concentrations (e.g., 1 - 3 mg/L) 

delivered from various land uses in the Simple Method Model. The nonpoint source load 

allocations then became the difference between the load capacity and the sum of the background 

and wasteload allocations (Table 37). 

Table 37. Estimates of the BOD5 loading capacities, load allocations (LA), and wasteload allocations 

(WLA) for six sites in the Stillaguamish River basin and the estimated potential 

dissolved oxygen concentration. 

Water Body 

Load 

Capacity 

BOD5

(lbs /day) 

Background 

LA 

BOD5

(lbs /day) 

Nonpoint 

LA 

BOD5

(lbs /day) 

NPDES 

Permit Holder 

WLA 

BOD5

(lbs /day) 

Estimated 

Potential 

DO 

(mg/L) 

Portage Creek at 212th 300 210 70 Snohomish County 

WSDOT 

12 

8 

6.5 

Portage Creek at 43rd 250 100 8 Arlington 142 7 

Pilchuck Creek 890 350 330 Snohomish County 

WSDOT 

27 

179 

8 

March Creek 30 10 20 Snohomish County 

WSDOT 

Arlington 

0.02 

0.06 

0.7 

6.5 

Kackman Creek at 

252nd

10 5 4 Snohomish County 0.6 7 

Warm Beach Creek & 

Dike Pond 

30 20 8 Snohomish County 

Warm Beach 

WWTP 

1.4 

0 

8 

 

The Warm Beach facility has recently completed an upgrade. If the plant remains in Warm 

Beach Creek, its effluent characteristics must meet water quality criteria and show no measurable 

effect downstream in the Dike Pond. During some periods of the summer, Warm Beach Creek 

has no flow upstream of the Warm Beach Conference Center WWTP, so the effluent is not 

diluted. In such cases, Ecology policy states that the water quality standard must be met at the 

end of the outfall (Bailey, 2002). When Warm Beach Creek is flowing, it does not meet the 

Class A criterion. Since no further degradation is permitted downstream, the BOD wasteload 

allocation must be zero, unless the facility can show that its effluent BOD and DO concentrations 

do not cause further degradation 

Specific load allocations and wasteload allocations for sources along the two reaches of the 

mainstem Stillaguamish River identified with DO problems cannot be calculated. The impact of 

the Old Stillaguamish River Channel on the Stillaguamish varies with tide phase, flow volumes 

and dispersion, and the water quality characteristics of the two bodies of water. Sources of 

nitrogen, phosphorus, and carbon affecting DO in the reach of the Stillaguamish River from 

Arlington to the Interstate 5 (I-5) bridge were modeled using QUAL2Kw (Table 32). The results 

were not accurate enough for the complexity of the problem. 
Page 114 Stillaguamish Fecal and DO TMDL Submittal Report

The load allocation of water with low DO concentrations from the Old Stillaguamish River 

Channel to the mainstem Stillaguamish River is zero. If the newly-installed tide gate at the 

bifurcation point does not eliminate the flow of deoxygenated water from the Old Stillaguamish 

Channel, then a new load allocation will be determined when the dissolved oxygen TMDL is 

completed for the Old Channel. 

Loading capacity analyses of the Stillaguamish River between Arlington and the I-5 bridge 

concluded that loading under natural conditions could not be calculated at this time using the 

QUAL2Kw model. The analyses also showed that although they could not be accurately 

quantified, low-flow period loads of nutrients and BOD from the upper basin, Arlington WWTP, 

unidentified nonpoint sources, Armstrong Creek, and March Creek have an effect on the 

DO concentrations in the reach (Table 32). A target minimum DO concentration of 7 mg/L was 

recommended to protect beneficial uses in the reach, and to stimulate management plans and 

activities limiting anthropogenic inputs of carbon, nitrogen, and phosphorus when the dissolved 

oxygen is completed for the Old Chanel (approximately 2007 to 2008). 

Nutrient (carbon, nitrogen, and phosphorus) loads affecting the reach will require closer 

management to minimize DO losses in the river and to meet the estimated potential 7 mg/L 

concentration during the critical season. For example, Arlington WWTP effluent appears to 

have an effect on downstream DO concentrations and stimulates periphyton biomass production. 

The current NPDES permit for the Arlington WWTP five-day BOD load has technology-based 

limits, and nitrogen and phosphorus loads are not addressed. If seasonal permit limits were 

‘performance-based’ to better reflect the effluent BOD5 quality since the 1998 upgrade (less than 

10 mg/L) and if nitrogen and phosphorus monitoring and treatment planning were written into 

the permit, then better management alternatives for the effluent treatment and disposal could be 

developed when natural conditions in the river are better defined. 

 

Phosphorus loading in both the lower North Fork and the South Fork Stillaguamish has increased 

according to trend analyses performed on the Ecology monthly monitoring data. The 

QUAL2Kw model simulations also suggested that nonpoint and tributary sources in the reach 

can be significant during low-flow periods. The DO target may not be met until nutrient loads 

from these sources are reduced or excluded. Phosphorus reductions are also recommended to 

decrease pH maxima in the North Fork Stillaguamish River. The Clean Water District’s 

nonpoint management plans and implementation activities should direct resources at the 

phosphorus loading problem in this area. 

pH 

The following sites should be reassessed to determine natural seasonal or event-based pH 

conditions once the anthropogenic sources of oxygen-demand or low pH stormwater are reduced 

or eliminated as fecal coliform and dissolved oxygen loading capacities are met: 

• Stillaguamish River above Arlington at the confluence of the North and South forks 

• Pilchuck Creek 

• Kackman Creek 

• March Creek 
Stillaguamish Fecal and DO TMDL Submittal Report Page 115

Meeting conditions for natural conditions may be indirectly attained when targets for fecal 

coliform or dissolved oxygen are met. Stormwater wasteload allocations and nonpoint load 

allocations have already been set in the three tributaries to meet loading capacities for dissolved 

oxygen and fecal coliform (Tables 35 and 37). The fecal coliform loading reductions for the 

mouths of the South Fork and North Fork Stillaguamish River, and their accompanying 

stormwater wasteload allocations, should be sufficient to bring pH values into compliance at the 

confluence of the forks above Arlington during storm events (Tables 33 and 35). Since the 

potential sources of low pH from decomposition of organic materials are similar to those that 

may contain fecal bacteria and oxygen-demand, the reductions in place should help attain the 

best potential pH values. Wetland drainage and groundwater inputs should be included as part of 

the determination of natural conditions in the tributaries, as should seasonal instream organic 

material cycling processes. 

The North Fork Stillaguamish River at Whitman bridge to Cicero bridge (NFRKM 28.3 to 

NFRKM 15.2) is affected by elevated pH values. Reducing the total phosphorus load may 

improve the July through September low-flow pH conditions by decreasing the periphyton 

biomass responsible for the elevated pH values. Bringing the median seasonal total phosphorus 

concentration to 0.01 mg/L and reducing the median seasonal load from 41 lbs/day to 20 lbs/day 

will be equal to the 1987 to 1995 seasonal average. The load is allocated to background 

(6 lbs/day) and nonpoint sources (14 lbs/day). 

Table 38. Load allocations for Total Phosphorus in the North Fork Stillaguamish River to reduce 

periphyton biomass and address elevated pH measurements. 

Water Body Loading Capacity 

(Total Phosphorus) 

Background Load Non-Point Load Target Value 

Total Phosphorus 

North Fork 

Stillaguamish 

River 

(km 15.2-28.3) 

20 lb/day 6 lb/day 14 lb/day 0.01 mg/L 

(median seasonal 

value) 

Arsenic and Mercury 

Arsenic and mercury in the basin are from natural sources without enrichment from 

anthropogenic sources. The metals are highly associated with suspended solids. Both the South 

Fork and North Fork have documented natural erosion areas with total suspended solids (TSS) 

loads that have created sedimentation problems in downstream channel reaches (WCC, 1999). 

Continued work reducing the TSS loading from these areas and basin-wide would help decrease 

arsenic and mercury loading. No amount of reduction would allow arsenic concentration to meet 

EPA human-health criteria. Therefore, all loads for arsenic and mercury are allocated to 

background. 

To better manage incidental mercury from sediment, a target TSS concentration to limit mercury 

concentrations greater than the aquatic toxicity criterion could be based on the regression 

equation relating TSS in mg/L to mercury in ug/L: 

 Mercury = 0.0011 x TSS 0.5704 

An average four-day TSS concentration of 65 mg/L would limit the mercury concentration to 

0.012 ug/L. The TSS concentrations are not well correlated with discharge at any of the sites. 
Page 116 Stillaguamish Fecal and DO TMDL Submittal Report

Sudden increases in runoff generally create increases in TSS. A TSS loading capacity was not 

developed. 

Based on very few samples collected from the North Fork Stillaguamish near Darrington (n=4), 

the TSS surrogate concentration of 65 mg/L would not be appropriate there. Based on a linear 

correlation (r2 = 0.93) for the four data points, a TSS concentration of 13 mg/L for the North 

Fork near Darrington would limit mercury to 0.012 ug/L. A four-day average TSS concentration 

of less than 13 mg/L at these sites should result in mercury concentrations within the chronic 

toxicity criterion. 

Margin of Safety 

This TMDL evaluation requires a list of implicit and explicit expressions margins of safety 

(MOS) used to determine the loading capacity, load allocations, and wasteload allocations. The 

MOS magnitude varies with the confidence in the data available and the analytical tools used. 

The MOS is the means by which the analysis accounts for the uncertainty about the relationship 

between pollutant loads and the receiving water quality (EPA, 2001). To protect beneficial uses 

to the fullest extent, a conservative approach must be taken so that an error in load allocations 

and wasteload allocations does not cause impairment of the water body. The following are 

conservative assumptions that implicitly or explicitly contribute to an MOS. 

• The statistical rollback method was applied to fecal coliform data from the most critical 

season, and the resultant target geometric means are more stringent than the Washington 

State criterion of 100 cfu/100 mL. This is an explicit assumption for the MOS. 

• Since the variability in fecal coliform counts during the critical season when storm-event data 

are included is usually quite high, the targets are more restrictive. This is especially true at 

sites with fewer than 20 data. These factors are implicit contributions to the MOS. 

• The fecal coliform loading capacities and target geometric means for the North Fork 

Stillaguamish River at Twin Rivers and the Stillaguamish River at Interstate 5 were 

conservatively calculated to include the loading from unidentified sources located along 

upstream reaches. These are implicit contributions to the MOS. 

• The fecal coliform loading capacities and target geometric means for three small tributaries 

that discharge directly to Port Susan are based on more restrictive Class AA freshwater 

criteria rather than Class A criteria. This is an explicit contribution to the MOS. 

• The cumulative freshwater fecal coliform loads to Port Susan during the critical season will 

be reduced by 77 percent under the TMDL targets, even if instream die-off is not considered. 

Port Susan sites require fecal coliform reductions of 2 percent – 60 percent. The difference is 

an explicit MOS. 

• The treatment plant wasteload allocations for fecal coliform do not consider dilution in a 

mixing zone during a 7seven-day, ten-yr (7Q10), low-flow event at full permit capacity. 

This is an explicit MOS. 

• The targets for minimum dissolved oxygen concentrations in areas considered to have natural 

sources of low dissolved oxygen are set to be protective of supporting most phases of the 

salmon life cycle under the worst habitat conditions. Therefore, sites located in areas with 
Stillaguamish Fecal and DO TMDL Submittal Report Page 117

better habitat and water movement should have all phases of the life cycle protected. This is 

an implicit MOS. 

• The stormwater model assumes that 90 percent of the rainfall creates runoff, and the 

concentrations of fecal coliform and BOD are in the upper range of mean values in technical 

literature. In western Washington, the low intensity of many rain events does not deliver 

runoff. Therefore, higher fecal coliform and BOD loads are predicted by the model than are 

actually delivered. The wasteload allocations and load allocations based on these model 

results are probably more restrictive. This is an implicit assumption for the MOS. 

• Some of the sites recommended for pH TMDL-related activities were identified by applying 

a 0.2 standard unit (s.u.) safety factor to the 10th and 90th percentile statistics. The 

application of the safety factor is an explicit addition to the margin of safety. 

Summary Implementation Strategy 

Implementation Overview 

The purpose of this summary implementation strategy (SIS) is to describe how the waters 

addressed by the Stillaguamish River Watershed Fecal Coliform, Dissolved Oxygen, pH, Arsenic 

and Mercury Total Maximum Daily Load Study (Ecology, July 2004) can achieve water quality 

standards. This SIS complies with the federal mandate of the Clean Water Act (CWA), state 

laws to control point and non-point source pollution, and with the Memorandum of Agreement 

between the U.S. Environmental Protection Agency and Washington State Department of 

Ecology (EPA, 1997). 

The Ecology TMDL study addresses stream reaches in the Stillaguamish watershed and marine 

waters of Port Susan that were placed either in 1996 or 1998 on the state’s list of impaired waters 

(303[d] list, now called the Water Quality Assessment); see Table 8. As required by federal 

water quality regulations, these waters then must be evaluated through the total maximum daily 

load (TMDL) process, which develops an estimate of the amount of a particular pollutant that a 

water body can handle without violating state water quality standards. Implementation, the 

second part of the TMDL process, starts with writing a summary implementation strategy, or 

plan of activities and programs to be carried out to reduce the pollutants. 

In this Strategy, implementing agencies and organizations in the Stillaguamish watershed will 

use existing regulations and programs to reduce high bacteria concentrations and address 

dissolved oxygen deficits and elevated pH. In addition, this SIS identifies additional resources 

that will be needed to reduce pollutants and improve water quality. After EPA approves this 

TMDL, these agencies and organizations will work with other interested parties to help Ecology 

develop a detailed implementation plan. The plan will recommend specific actions to take so 

that the river, its tributaries, and Port Susan can meet water quality standards in the future. A 

preliminary list of proposed implementing activities and initiatives, and a description of the 

adaptive management process, are the start for the detailed implementation plan and are included 

this strategy. 
Page 118 Stillaguamish Fecal and DO TMDL Submittal Report

The target date for meeting water quality standards for fecal coliform bacteria, dissolved oxygen, 

and pH is 2013 (8 years). This estimate is based on the likely need for a series of water quality 

monitoring efforts focusing on specific sub watersheds to better target failing septics and other 

nonpoint sources of bacteria, biochemical oxygen demand (BOD), and nutrients, with time 

required following identification for corrections to be implemented. This estimated target date 

also considers the time required for funding and planning of large, technically complex projects 

to address sediment loading. 

Impairments Leading to the TMDL, and TMDL Development

The Stillaguamish River, several of its tributaries, and Port Susan were included on Washington 

State’s 1996 and 1998, 303(d) lists because of violations of one or more water quality criteria 

(Table 8). This document includes the TMDL study that was conducted to address those listings 

and that includes recommendations for specific reductions of pollutants so that these waters, and 

additional water bodies found to be impaired during the study (Table 9), will meet water quality 

standards. 

Figures showing the location of monitoring sites in the lower watershed and Port Susan, along 

the mainstem, and on the North Fork and South Fork are provided in Appendix C. Monitoring 

was conducted in 2000 and 2001 for conventional parameters including fecal coliform bacteria, 

and dissolved oxygen. Most monitoring was conducted monthly. However, additional 

monitoring targeted storm events, to assess impacts of stormwater on river water quality, and 

diurnal sampling was conducted in some reaches in order to assess day and night changes in 

dissolved oxygen. 

The study recommends reductions (load allocations) in fecal coliform bacteria from non-point 

sources at 34 locations throughout the watershed (Tables 33 and 34). Land uses associated with 

these locations include urban areas where stormwater may be a purveyor of bacteria; residential 

areas not served by sewers, where on-site septic system failures may contribute; and farms 

ranging from small “hobby” farms with few animals to livestock and dairy operations. 

Some of the locations requiring fecal coliform bacteria reductions receive stormwater drainage 

either from adjacent roadways or city stormwater infrastructure. Jurisdictions with responsibility 

for stormwater drainage include Washington State Department of Transportation (WSDOT) and 

Snohomish County, which have NPDES Phase I stormwater permits; and the city of Arlington, 

which will be a permittee under Ecology’s Phase II NPDES Municipal Stormwater Permit, 

expected to be issued in 2005. These three jurisdictions are assigned wasteload allocations 

(WLAs) for fecal coliform bacteria (Table 35). This means they will be required to implement 

best management practices (BMP) to reduce fecal coliform bacteria in their stormwater runoff in 

the watersheds listed in Table 35. 

In addition to the WLAs for fecal coliform for stormwater permittees, the TMDL recommends 

WLAs for WWTPs in the watershed (Table 36). 

Dissolved oxygen is the second parameter of concern in the watershed evaluated in this TMDL. 

Initially five locations in the watershed were included on the 1998 303(d) list (Table 8); 

however, additional monitoring conducted during the study indicated that other locations exhibit 
Stillaguamish Fecal and DO TMDL Submittal Report Page 119

low dissolved oxygen during low flow periods. As a result, nine locations are identified in the 

study as requiring reductions in biolochemical oxygen demand (BOD). Six of these receive 

stormwater drainage, so wasteload allocations (WLA) have been assigned to Snohomish County; 

city of Arlington; and/or WSDOT, depending on which of these stormwater permittees is 

responsible for drainage infrastructure at the six locations (Table 37). The remaining three 

locations are affected by nonpoint BOD loading only (also Table 37). 

The TMDL study results for pH suggest that low pH values in Pilchuck, Kackman, and March 

Creeks, are storm event related. The study recommends continued monitoring to confirm this 

relationship. The low pH values likely result from decomposition of organic material introduced 

to the river and creeks through storm runoff. It is expected that the wasteload allocations will 

reduce inputs that are also supplying organic material. Similarly, the efforts required to reduce 

nonpoint sources of bacteria are likely to be effective in reducing some organic loading to the 

river. As a result, no load allocations were established to address the low pH measurements. 

Review of the data that led to the 1996 and 1998 pH listings for the South Fork Stillaguamish at 

Arlington has led to a recommendation that this reach be de-listed.

The elevated pH measurements made in North Fork Stillaguamish River between Whitman 

Bridge and Cicero generally occurred during July-September (low flow season). Reductions in 

total phosphorus loading are required through load allocations (Table 38); reducing this load is 

expected to decrease the periphyton biomass responsible for the elevated pH values. 

For arsenic and mercury, the additional measurements collected during the course of the study 

were evaluated with respect to the geology of the region. Both arsenic and mercury are highly 

associated with suspended solids. Both appear to reflect natural background sources in the basin; 

no other sources were identified. Consistent with a statewide review of arsenic that recommends 

delisting unless an anthropogenic source is identified, this TMDL recommends delisting arsenic. 

For mercury, which under moderate flow conditions was measured at some locations at 

concentrations above the 4-day chronic toxicity criterion, a load allocation was set for total 

suspended solids (TSS). Ongoing work in the watershed to reduce TSS loading from natural and 

human-caused erosion should result in reduced concentrations of mercury. 

Implementation Plan Development

The TMDL studies addressing fecal coliform bacteria, dissolved oxygen, and pH impairments in 

the Stillaguamish watershed (Ecology July 2004) include recommendations for programs and 

actions that will help improve water quality and enable these waters to meet state water quality 

standards. This section relates these needed programs and actions to the local agencies, Tribes 

and watershed organizations that can undertake them. These organizations have influence, 

regulatory authority, information, resources or other involvement in administering natural 

resource programs in the Stillaguamish watershed. Through meetings with these organizations 

in 2005 and 2006, Ecology will coordinate development of the detailed implementation plan. A 

preliminary list of projects, some requiring new funding, have been identified that will begin to 

address the pollutant reductions required by this plan. 
Page 120 Stillaguamish Fecal and DO TMDL Submittal Report

Approach for Non Point Sources 

For nonpoint sources, the TMDL establishes load allocations (LAs) to each river segment and 

tributary so that these water bodies will meet standards. (For some locations, allocations needed 

to be established for both point sources and nonpoint sources.) The percent reductions in fecal 

coliform bacteria, and nutrient or BOD loads in the case of dissolved oxygen (DO), are those 

required for the water body to meet standards under critical conditions of flow and season, which 

were identified for each parameter in the TMDL (see Tables 33-38). 

This section summarizes recommendations for reducing nonpoint sources, through a variety of 

BMPs appropriate for different types of sources, to achieve the TMDL goal of meeting water 

quality standards for fecal coliform bacteria and dissolved oxygen. 

Fecal Coliform Bacteria 

The major source of fecal coliform contamination in most of the water bodies in the watershed is 

nonpoint runoff from mixed land uses. Additional investigation is required to determine whether 

sources are failing septic systems, improper management of manure, pet waste, sewage 

infrastructure failure, stormwater, or wildlife. 

It can take time to resolve and correct fecal coliform contamination of waters in mixed land use 

situations, i.e., where the immediate sources of bacteria have not been identified. However, 

where funding is available and local agencies are committed to resolving these issues, significant 

reductions in stream fecal coliform have been achieved. An example is Kitsap County Health 

District’s Dogfish Creek project in Poulsbo, Kitsap County (KCHD, 2004). Funded partly by an 

Ecology Centennial Grant, the project included three years of sampling, public outreach, 

coordination with Kitsap Conservation District to address potential livestock sources, a door-todoor survey of 145 homes for potential septic system failures, work with individual property 

owners to repair or replace septic systems, and review of potential stormwater drainage impacts. 

Over the four-year effort, the annual geometric mean measurement of fecal coliforms was 

reduced from 243 to 62 in the main channel of Dogfish Creek. 

The 36 locations in the Stillaguamish watershed identified as requiring reductions in nonpoint 

sources of fecal coliform (Tables 8 and 9) can be grouped into eight sub watersheds for 

“community outreach/source identification and correction” projects similar to KCHD’s Dogfish 

Creek project. 

• Warm Beach residential area including Martha Lake Creek and unnamed creek #0456. 

• Nonpoint polluted water bodies in vicinity of Warm Beach Camp and Conference Center. 

• Tributaries to Old Stillaguamish Channel: Jorgenson Slough/Church Creek, Irvine 

Slough, West Pass and South Pass. (Prior to development of Old Stilly Channel TMDL, 

water quality in these tributaries should be addressed through nonpoint source 

identification and correction.) 

• Glade Bekken Creek. 

• Pilchuck Creek. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 121

• March-Fish-Portage Creeks-Stillaguamish mainstem (both up- and downstream of I-5). 

• Harvey-Armstrong-Kackman Creeks. 

• Lower North Fork, lower South Fork, and Jim Creek. 

Depending on the sources identified by carrying out these more geographically focused projects, 

the ultimate corrections will likely include repair and replacement of failing on-site septic 

systems and agricultural best management practices. Some of the creek systems in the above 

groupings have stormwater drainages; potential corrective actions (best management practices) 

for these systems are noted below. 

Dissolved Oxygen 

Water quality monitoring data from the Ecology July 2004 TMDL study included measurements 

of dissolved oxygen that were lower than the water quality standard during low flow, often late 

summer or early fall periods (critical seasonal condition) at the following. 

• Warm Beach Creek above WWTP, and a pasture drain and pumped drainage from a 

stormwater collection pond in the floodplain adjacent to the Warm Beach Camp and 

Conference Center WWTP. 

• Stillaguamish River at bifurcation with Old Stillaguamish Channel. 

• Pilchuck Creek at Jackson Gulch Road. 

• Portage Creek – several locations. 

• March Creek. 

• Kackman Creek. 

• Stillaguamish River below Arlington (RM 13). 

Low dissolved oxygen is often correlated with warm stream temperature; however, in the 

locations listed above there may be contributing factors of: 

• High nutrient loading leading to growth of periphyton (algae) that consume more oxygen 

during night-time respiration than they produce during day-time photosynthesis. 

• High organic loading that carries a high biological oxygen demand. 

• Significant inflow of ground water, which often has low dissolved oxygen. 

Some of the reaches with dissolved oxygen impairments will likely be improved through 

working with livestock owners to ensure that nutrients associated with manure are not reaching 

the river and creeks. Nutrients can also be associated with on-site septic waste or with fertilizer 

use. Riparian streambank and channel improvements that improve flow, filter nutrients from 

adjacent land uses, and add shade, can improve dissolved oxygen conditions. Where high 

groundwater inflow that is depleted in dissolved oxygen is causing the impairment, it is a natural 

condition not subject to remediation or load allocations. 
Page 122 Stillaguamish Fecal and DO TMDL Submittal Report

In the case of the low DO location at RM 13 in the mainstem below Arlington, the TMDL study 

suggests that multiple causes, including a potential role played by nutrients from the Arlington 

WWTP, may contribute. To attempt to sort out these causes and design solutions that will be 

effective, a two year monitoring study of nutrient and fecal loading from stormwater, the 

WWTP, and in the South Fork above Arlington is being planned by Ecology with assistance 

from the city of Arlington. 

Local and Tribal governments can provide support for maintaining and increasing the riparian 

integrity of streams in the watershed through education of citizens and adoption and enforcement 

of critical areas ordinances and shoreline management plans that protect riparian buffers. 

pH 

Occurrences of elevated pH in the North Fork Stillaguamish (see page 105, Loading Capacity 

section) may be associated with high levels of periphyton production. Reducing nutrient inputs, 

particularly phosphorus, by educating landowners along this reach of the river about BMPs and 

proper septic maintenance should begin to correct this problem. 

Metals – Arsenic and Mercury 

 

Because of the strong association of mercury and arsenic concentrations in the river with 

suspended solids, measures that address the river’s high sediment load should be assigned high 

priority in implementation planning and grant application processes. These should include better 

erosion control measures and projects that divert the river’s course away from some of the large 

landslides that continuously supply sediment to the river, 

Approach for Point Sources 

This TMDL assigns wasteload allocations to point sources of fecal coliform bacteria (WWTPs, 

Table 36) and to point sources of BOD loading. This reduces dissolved oxygen in streams below 

roadways (jurisdictions with NPDES Phase I and future Phase II stormwater permits, Table 37). 

(Current WWTP permit information and the basis for proposed limits developed in this TMDL 

are provided in Appendix B.) Note that wastewater treatment plant permits will reflect these 

TMDL requirements in a different way than the NPDES stormwater permits. While the WWTP 

permits are expected to incorporate the numeric effluent limits recommended in this TMDL 

when the permit is reissued, stormwater permits are not expected to have numeric limits related 

to the wasteload allocations. EPA guidance (Wayland and Hanlon, 2002) indicates that 

stormwater permittees will address TMDL requirements through Best Management Practices. 

Because the loading capacities of the river and streams in this study were determined for critical 

conditions of warm stream temperature and low flow in late summer and fall, the WLAs are 

established for these critical seasonal conditions. 

Arlington WWTP 

The TMDL proposes that Arlington WWTP permit limits for fecal coliform be reduced from 

200/400 (maximum monthly average and maximum weekly average cfu/100 ml) to 39/128 

(monthly/weekly). This Strategy suggests that the appropriate time for the new limit to be 
Stillaguamish Fecal and DO TMDL Submittal Report Page 123

included in the permit is in the next permit cycle (2008). This will provide a three-year period to 

assess changes in the loading of fecal coliform bacteria in the receiving waters and allow time for 

BMPS related to stormwater quality and cleanup of nonpoint sources upstream to be 

implemented. If these other sources of fecal coliform are not reduced so that the river meets 

water quality standards by 2008, then the proposed reduced permit limits will be applied during 

re-issuance of the permit. 

Because the dissolved oxygen minimum 6.8 km downstream cannot be directly attributed to the 

WWTP, there is no change proposed for the current permit limit for biolochemical oxygen 

demand (BOD). New information from a two-year nutrient, fecal coliform and stormwater 

monitoring program during the seasonal low flow period (see Identified Needs and Early Action 

Proposals) will help determine whether additional treatment is needed at this facility. 

Warm Beach Christian Conference Center WWTP 

This TMDL allocates a zero-BOD wasteload allocation to the Warm Beach Christian Conference 

Center WWTP discharge due to low dissolved oxygen in the receiving waters (a small creek that 

drains to a flood control district drainage pond). As a result, the conference center is conducting 

a feasibility study of two alternative discharge locations: a piped discharge to Hat Slough near 

the South Branch channel, and a land-based drip irrigation system. The WWTP is operating 

under an extended discharge permit. The permit will be reissued in 2005. 

Indian Ridge Corrections Center WWTP 

No change is proposed to the current permit limits for Indian Ridge WWTP, because the 

condition of the receiving waters (Jim Creek) at the point of discharge is not impaired. 

Stormwater – City of Arlington 

The city of Arlington is expected to be one of a number of smaller cities throughout Washington 

State that will be covered under Ecology’s Phase II NPDES Municipal Stormwater Permit. 

Arlington filed its permit application in 2003; the Phase II permit is expected to be issued 

in 2006. 

Based on this TMDL, Arlington will need to develop as part of its municipal stormwater 

program a strategy for addressing:

• The fecal coliform reductions required for Portage Creek at 43rd, March Creek;, and 

South Fork Stillaguamish at mouth. 

• The dissolved oxygen impairments at the Portage Creek and March Creek locations. 

To ensure that the storm drains do not convey excessive bacteria, nutrients, and oxygendemanding material, the city should make sure that pollution-prevention steps are taken (illicit 

discharge detection, pet waste stations, more frequent street cleaning, and/or storm vault 

cleaning) or that treatment occurs prior to discharge. 
Page 124 Stillaguamish Fecal and DO TMDL Submittal Report

Stormwater – Snohomish County 

Snohomish County is covered by Ecology’s Phase I NPDES Municipal Stormwater Permit. 

Under the load allocations derived from road area in this TMDL, Snohomish County must 

address pollutants in stormwater drainage as specified in the following: 

• Fecal coliform reductions required for Fish, Harvey, Jim, Portage, Lake Martha, 

Unnamed #0456, Glade Bekken, Pilchuck, March, Armstrong, and Kackman creeks, and 

Warm Beach Dike Pond, and North Fork and South Fork of the Stillaguamish River at 

their confluence. 

• Dissolved oxygen impairments at Portage, Pilchuck, March, Kackman and Warm Beach 

creeks. 

To ensure that the county road storm drains do not convey excessive bacteria, nutrients, and 

oxygen-demanding material, the county should take pollution-prevention actions such as illicit 

discharge detection, retrofits of residential stormwater detention facilities, reviews of road 

maintenance and stormwater detention BMPs, and identification and implementation of drainage 

infrastructure improvements. 

Stormwater – WSDOT 

Washington State Department of Transportation (WSDOT) is a jurisdiction covered by 

Ecology’s Phase I NPDES Municipal Stormwater Permit. Based on this TMDL, WSDOT will 

need to show that it has taken steps to address: 

• Fecal coliform reductions required for Portage, Pilchuck, March and Armstrong creeks, 

and North Fork of the Stillaguamish River at its confluence with South Fork. 

• Dissolved oxygen impairments at Portage, Pilchuck, and March creeks. 

To ensure that the state highway storm drains do not convey excessive bacteria, nutrients, and 

oxygen-demanding material, WSDOT should make sure that pollution-prevention steps are taken 

(illicit discharge detection, more frequent highway cleaning, working with local governments to 

ensure that pet waste, farming practices, and septic systems are being appropriately managed) or 

that treatment occurs prior to discharge. 

Identified Needs and Early Action Proposals 

Stillaguamish watershed organizations, agencies, and Tribes are actively engaged in projects that 

will directly or indirectly lead to improvements in river and stream water quality. Appendix E 

includes a preliminary tabulation of projects that have recently been completed. However, 

despite this indication that much worthwhile effort is ongoing in the watershed, the five-year 

review of data that was undertaken in this TMDL suggests that fecal coliform impairments are 

widespread and not readily solved. It is likely that while improvements are occurring in some 

areas, other changes in the watershed may be associated with degradation of water quality. Such 

changes include the effects of population growth, increasing housing density, and increases in 

impervious area. And despite fewer commercial livestock operations, an increase has occurred 

in hobby farms, which could be associated with negative impacts on water quality. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 125

High priority actions that could indirectly lead to fecal coliform reductions are:

• Commitment by the Snohomish Health District to securing funding so that this agency, 

with its regulatory authority over septic systems will have the resources to assist sourceidentification monitoring/fecal reduction efforts in seven sub watersheds. Health District 

staff have indicated that if data are available to narrow down potential fecal coliform 

sources to a very small number of properties - 2 to 5 - then district sanitarians could carry 

out the necessary investigation and enforcement actions (K. Plemel, personal 

communication, September 2004). 

• Understanding by property owners of their responsibility to properly maintain on-site 

septic systems. Additional basin-wide education and outreach will be necessary. 

Projects recently funded or proposed for future funding are listed in Table 39. 

Table 39. Preliminary Proposals for Improving Water Quality

Project Title River 

Segment 

Parameter 

Addressed 

Organization Date 

Started/Completed 

Steelhead Haven 

Landslide Remediation 

North Fork Temperature, 

turbidity, arsenic 

and mercury 

(metals associated 

with sediments) 

Stillaguamish 

Tribe 

Approved for CCWF 

2004; Salmon Recovery 

Funds Dec 2005 

Snohomish County Septic 

Systems 

Pilot projects 

to include 2 

Stillaguamish 

sub 

watersheds 

Fecal coliform 

bacteria 

Snohomish 

Cty SWM 

with 

Snohomish 

Health 

District 

Submitted for 

FY06 Centennial 

Clean Water Funds; 

rated well in Jan 

2005 Project 

Rankings 

Harvey Armstrong & 

Fish Creeks Sub 

watersheds 

Harvey, 

Kackman, 

Armstrong, 

Fish Creeks 

Fecal coliform 

bacteria 

Snohomish 

Conservation 

District 

Submitted for FY06 

Centennial Clean Water 

Funds; rated well in Jan 

2005 Project Rankings 

Portage Creek Water 

Quality Improvement 

Portage Creek Dissolved oxygen 

and fecal coliform 

bacteria 

Stillaguamish 

Tribe 

Funded (Centennial 

Grant program) 

Receiving Water Quality 

and Stormwater Loading 

Study 

Mainstem 

Stillaguamish 

River and 2 

storm outfalls 

Dissolved oxygen 

and fecal coliform 

bacteria 

City of 

Arlington and 

Ecology 

Proposed for FY06 

Ecology funding and 

city of Arlington 

resources 

Revisions to City 

Wastewater and 

Stormwater 

Comprehensive Plans; 

City Water Conservation 

Plan and Watershed & 

Wellhead Protection Plan 

Mainstem 

Stillaguamish 

River and 

Portage Creek 

Dissolved oxygen 

and fecal coliform 

bacteria 

City of 

Arlington 

2005 
Page 126 Stillaguamish Fecal and DO TMDL Submittal Report

Cost Estimates for Water Cleanup Projects 

This section provides some approximate costs associated with the water quality improvement 

projects that are likely to be undertaken to implement this strategy. We did not attempt to 

estimate the cost of programs that may need to be undertaken by NPDES permittees, the 

WWTPs and jurisdictions covered by stormwater permits. 

The cost of addressing nonpoint fecal coliform pollution throughout the watershed, using a grantfunded approach to conduct source identification/public outreach/septic correction and 

agriculture BMP projects can be calculated (similar to Kitsap County Health District’s Pollution 

Identification and Correction [PIC] program): 

o 7 sub watersheds x $176,000 per sub watershed = $1.23 million 

(The figure of $176,000 is the approximate cost of one Kitsap County PIC project [Dogfish 

Creek] that achieved fecal coliform cleanup for about ten stream-miles; note that project costs 

vary with number of monitoring stations needed, housing density, type of septic and sewage 

infrastructure, and other variables.) 

This cost estimate is provided to give some indication of the level of effort and financial 

investment that may be required to meet the goals of the TMDL. In some cases, certain types of 

water quality improvements can be accomplished for less money using volunteer labor or 

through county-wide educational programs that are not as localized as a PIC project. 

Information and ideas about more cost-effective ways to accomplish these projects are welcome. 

Organizations with Programs to Improve Water Quality 

Tribes, local agencies, and Stillaguamish watershed organizations have ongoing programs that 

will assist in making improvements to water quality in the Stillaguamish basin. This section 

describes the capabilities of each organization as they relate to on-the-ground water quality 

projects that will reduce fecal coliform bacteria, improve dissolved oxygen conditions, and 

reduce stream temperatures. 

Stillaguamish Implementation Review Committee (SIRC) 

The Stillaguamish Implementation Review Committee (SIRC) is a watershed-based local 

stakeholder group established in the early 1990s. Its mission is to restore and maintain a healthy, 

functioning Stillaguamish River watershed by providing a local forum in which agencies, 

organizations, communities, and the public can engage in a collaborative watershed-based 

process of decision-making and coordination. Its initial focus was to oversee implementation of 

the 1990 Stillaguamish Watershed Action Plan, which included 71 recommendations for 

controlling non-point pollution in the watershed. 

In the mid-1990s, the SIRC added salmon habitat restoration issues to its scope. Since 1999, 

with leadership from the Stillaguamish Tribe and Snohomish County, the SIRC has served as the 

local citizens’ committee for recommending prioritized lists of salmon habitat restoration 
Stillaguamish Fecal and DO TMDL Submittal Report Page 127

projects to the Washington State Salmon Recovery Funding Board. The SIRC has final 

oversight authority for lead entity projects, including salmon habitat project lists and the habitat 

restoration work schedule. 

Currently, the following are member organizations of SIRC: 

• City of Arlington 

• City of Stanwood 

• Stillaguamish Clean Water District Board 

• Federation of Fly Fishers 

• Mainstem Stillaguamish community 

• North Fork Stillaguamish community 

• South Fork Stillaguamish community 

• Pilchuck Audubon Society 

• Snohomish Conservation District 

• Snohomish County Council 

• Snohomish County Noxious Weed Control Board 

• Snohomish County Planning and Development Services 

• Snohomish County Surface Water Management 

• Stillaguamish Flood Control District 

• Stillaguamish Grange 

• Stillaguamish Tribe 

• Stillaguamish-Snohomish Fisheries Enhancement Task Force 

• Twin City Foods 

• Tulalip Tribes 

• U.S. Forest Service 

• Washington Dairy Federation 

• Washington Dept. of Ecology 

• Washington Dept. of Fish & Wildlife 

• Washington Dept. of Natural Resources 

• Washington Farm Forestry Association 

• WSU Cooperative Extension 

In June 2004, SIRC issued the Stillaguamish WRIA 5 Draft Chinook Salmon Recovery Plan 

(SIRC, 2004) which recommends an integrated strategy for protecting and restoring Chinook 
Page 128 Stillaguamish Fecal and DO TMDL Submittal Report

salmon populations. The strategy includes recommendations for habitat restoration projects, 

compliance and enforcement of existing regulations, policy and regulatory coordination, 

preliminary commitments and conditions to achieve recovery objectives. monitoring and 

adaptive management, and public outreach and coordination. 

Clean Water District 

The Lower Stillaguamish Clean Water District was established in 1993 by Snohomish County 

Ordinance 96-080, Title 25 A, to improve drainage, water quality, and fish habitat/shellfish beds. 

This establishment occurred after the state Department of Health indicated, in response to a 

request, that water quality would not be good enough to open shellfish beds to commercial 

harvest. Parcels in the district are assessed an annual fee. Currently 33 percent of fees is 

allocated to the Snohomish Conservation District to perform services to reduce pollution; 59.1 

percent is allocated to water quality restoration activities administered by the Department of 

Public Works, including funding of the Stillaguamish Steward position; and 7.9 percent is 

allocated to Department of Public Works for local water quality restoration projects that are 

recommended by the Clean Water District Advisory Board. 

City of Arlington 

The city of Arlington, population 13,700, borders the South Fork Stillaguamish River and a short 

extent of the mainstem, totaling about one mile of shoreline. Just below the confluence of the 

two forks, the city operates a 2-mgd wastewater treatment facility (WWTP) that discharges 

treated effluent to the river and a drinking water treatment facility serving more than 4,000 

connections. 

The city has adopted the 1992 Ecology Stormwater Manual and has applied for the Phase II 

General Municipal NPDES Stormwater permit. Arlington’s application shows that three out of 

twelve stormwater outfalls discharge directly to the mainstem Stillaguamish River and its South 

Fork (most other outfalls discharge to tributaries or ditches that also reach the river). The city’s 

stormwater management program includes an illicit discharge detection program. City staff are 

working with Ecology to develop a detailed water quality monitoring program that will address 

data gaps in the vicinity of the city’s WWTP identified in the Ecology July 2004 TMDL study. 

Through city efforts, vegetative plantings have been installed at 26 sites along about five miles of 

streambank within the city limits. These and other projects likely to lead to water quality 

improvements in the city’s drainages to the Stillaguamish are listed in Appendix E. 

Snohomish County Surface Water Management 

Snohomish County Surface Water Management (SWM) administers programs that contribute 

both to assessment of water quality in the Stillaguamish basin and programs that improve water 

quality. The SWM monitors water quality on a long-term basis at a number of sites county-wide

and, as resources allow, may conduct special monitoring programs. The county has monitored 

eight sites in the Stillaguamish basin monthly for water quality since 1994. In addition, targeted 

monitoring programs have been conducted at locations within the basin to assess the effect of 

small farm BMPs and riparian restoration projects. In 2001 SWM conducted a one-time 
Stillaguamish Fecal and DO TMDL Submittal Report Page 129

intensive fecal coliform sampling program targeting creeks, ditches, outfalls, and marine waters 

in the Warm Beach residential community in an effort to identify failing septic systems. 

SWM programs that directly benefit water quality in the Stillaguamish watershed include the 

following: 

• Snohomish County has a strong public outreach program, which consists of educational 

programs for students, teachers, and the general public. The county also has a native 

plant salvage program that generates hundreds of hours of volunteer time each year in 

watershed restoration projects. A full-time watershed steward is assigned to work with 

citizens on riparian restoration, small farm BMPs, and other water quality projects 

throughout the Clean Water District. 

• Snohomish County adopted a Water Pollution Control Ordinance (Chapter 7.53 SCC) in 

March 1998. The ordinance prohibits the discharge of pollutants to Snohomish County 

Streams. 

• Monthly monitoring of eight sites in the Stillaguamish basin for water quality since 1994; 

data are available on the internet at http://www.data.surfacewater.info. The county 

provides support to DOH to monitor South Skagit Bay for bacteria. 

• As part of Phase I NPDES Municipal Stormwater Permit requirements, the county 

identifies and inspects selected storm sewer outfalls in the Stillaguamish watershed, 

inspects residential stormwater detention facilities, maintains its storm sewer system, and 

identifies and implements drainage infrastructure improvements. 

Stillaguamish Tribe 

The Stillaguamish Tribe Natural Resources Department administers a number of programs that 

contribute to understanding of, and making improvements to, the watershed conditions that affect 

salmonid and other fish and shellfish resources of the Stillaguamish watershed and Port Susan. 

Programs include: 

• Leadership and support for the Stillaguamish Implementation Review Committee and its 

goals of increasing salmonid populations and improving water quality throughout the 

basin. 

• Water quality monitoring of Port Susan under a cooperative agreement with the 

Department of Health to determine commercial shellfish harvest classification. 

• Water quality monitoring at a number of locations throughout the watershed, including a 

study of the effects of a flow enhancing structure on the upstream end of the Old Stilly 

Channel. 

• Certification to negotiate CREP (Conservation Reserve Enhancement Program) contracts 

with landowners to plant riparian buffers and fence livestock away from streams to 

prevent or reduce fecal coliform pollution. 

• Banksavers Program, a for-profit native plant nursery that maintains native plant nursery 

stock and manages riparian planting and maintenance projects. 

• Operating a smolt trap on the Stillaguamish River to help determine numbers of coho and 
Page 130 Stillaguamish Fecal and DO TMDL Submittal Report

Chinook smolts. 

• Operating a hatchery on Harvey Creek. 

Snohomish Health District 

Snohomish Health District (SHD) has authority and requirements under Revised Code of 

Washington (RCW) to administer public health and on-site sewage programs in the county. In 

addition, Chapter 246-272 Washington Administrative Code (WAC) Rules and Regulations of 

the Washington State Board of Health for On-site Sewage Systems grants local health 

jurisdictions authority to administer the code. With this authority, SHD has established 

Snohomish Health District Sanitary Code Chapter 8.1: On-Site Sewage System Regulations, 

which includes rules and regulations covering: 

• Permitting of site evaluations, OSS designs, and installations. 

• Inspection of OSS installations during construction and at completion. 

• Investigation of complaints related to improper sewage treatment and disposal. 

• Maintaining an electronic database of existing OSS and As-Built drawings indexed by 

county property parcel number and street address. SHD intends to make this information 

available online in 2005. 

The SHD also administers regulations affecting pet waste disposal; under Ch. 3.1, Solid Waste 

Handling Regulations, pet waste may be placed in the garbage; buried on site at a depth of one 

foot or greater; or flushed down the toilet provided the property is serviced by sewer rather than 

an on-site septic system. 

Snohomish Conservation District. 

The Snohomish Conservation District (SCD) works throughout Snohomish County and on 

Camano Island with landowners and livestock owners in developing resource management plans 

for surface water quality protection. The SCD provides information and services related to 

riparian and instream restoration, soils, and nutrient management. In addition to trained staff 

SCD can provide technical assistance in soil science, hydrology, forestry, wetlands, and 

engineering through the Natural Resource Conservation Service (NRCS). 

The SCD provides technical assistance, farm plans, and cost-share funds for the implementation 

of BMPs using state and federal funding sources. TMDL-related BMPs that are recommended 

and implemented include fencing livestock out of streams, improving pasture and nutrient 

management, installing gutters to keep water away from barnyard areas, composting and storage 

of manure, and planting riparian buffers. These BMPs help prevent the transport of mud, 

nutrients and manure to surface waters, and improve watershed health overall. The SCD 

implements riparian restoration through the Conservation Reserve and Enhancement Program 

(CREP) and conducts water quality monitoring. 

Additional services the SCD is interested in providing, should resources be available, would 

assist in achieving the goals of this TMDL. These include: 
Stillaguamish Fecal and DO TMDL Submittal Report Page 131

• Water quality monitoring, education and outreach to landowners in sub-basins 

• Focused BMP effectiveness monitoring 

• Inventory of farms, including “animal census” information 

• Expanded financial assistance programs for farm planning and BMP implementation 

Stilly-Snohomish Fisheries Enhancement Task Force 

The Stilly-Snohomish Fisheries Enhancement Task Force (SSFETF) is a 501(c) (3) nonprofit 

corporation based in Everett. The mission of SSFETF is to ensure the future of salmon in the 

Stillaguamish and Snohomish watersheds. Since its beginning in 1990, the Task Force has 

developed community partnerships and strategies for restoring salmon habitat. It has conducted 

a number of volunteer planting events and stream restoration projects in the Stillaguamish 

watershed, including projects on Portage Creek and Glade Bekken Creek near Silvana. 

Tulalip Tribes 

The Tulalip Tribes are a sovereign nation with land use authority within their reservation in 

Marysville. Usual and Accustomed fishing areas include Port Susan and the Stillaguamish 

River. The Tribes’ Water Quality and Fisheries Department has, in the past, conducted water 

quality monitoring in the watershed and has an interest in targeting priority areas of the 

watershed and assessing success of implementation activities. The Tribes have supported a 

number of water quality, aquatic habitat, and fisheries-related studies of the Stillaguamish River. 

Washington State Department of Agriculture (WSDA) 

WSDA administers the Dairy Nutrient Management Act (Ch. 90.64 RCW), which required dairy 

farmers to have approved dairy waste management plans by July 1, 2002 and to implement the 

plans by end of 2003. WSDA has responsibility for agricultural operations with NPDES permits, 

including Animal Feeding Operations (AFOs) and Concentrated Animal Feeding Operations 

(CAFOs). Under its regulations, WSDA has authority to inspect dairies and other permitted 

operations on a regular schedule. In 2004, a WSDA livestock program water quality inspection 

program for western Washington dairies and livestock facilities was initiated. The program had 

lapsed during transfer of the DNMA inspection program from Ecology. Stillaguamish-basin 

dairy inspections were resumed in fall 2004 (J. Canaan, personal communication). 

Washington Department of Health 

The Department of Health (DOH) Shellfish Division, under authority of Chapter 43.70 RCW, 

monitors marine water quality in commercial shellfish growing areas. Monitoring for fecal 

coliform bacteria is conducted monthly by the Stillaguamish Tribe at 16 sites in and adjacent to 

Port Susan under a cooperative agreement with DOH for shellfish harvest classification. 
Page 132 Stillaguamish Fecal and DO TMDL Submittal Report

Ecology 

Washington State Department of Ecology has been delegated authority under the federal Clean 

Water Act by the U.S. EPA to establish water quality standards and enforce water quality 

regulations under Water Pollution Control Act, Chapter 90.48 RCW. In addition to this 

regulatory role, Ecology provides financial assistance to local governments, Tribes, and 

conservation districts for water quality projects and stream restoration. Projects that implement 

water cleanup plans are a high priority for funding. 

U.S. Environmental Protection Agency 

The EPA is responsible for reviewing and approving Ecology’s TMDLs and enforcement of the 

Clean Water Act. EPA provides funding for states and tribes to implement the Clean Water Act. 

Reasonable Assurances 

The goal of the Stillaguamish Watershed Water Cleanup Plan for bacteria, dissolved oxygen, pH, 

arsenic, and mercury is for the waters of the basin to meet the state’s Class A and AA water 

quality standards for these parameters. The following rationale helps provide reasonable 

assurance that the Stillaguamish Watershed water quality goals will be met by 2013. There is 

considerable interest and local commitment to improving and protecting water quality and 

restoring salmon habitat of the Stillaguamish River, for example: 

• The Stillaguamish Implementation Review Committee has identified water quality as one of 

its highest priorities as it seeks to protect and restore salmonid habitat throughout the 

watershed. Local government agencies and individual citizens are well represented and 

involved at SIRC meetings and at Clean Water District meetings. Given a choice of three 

levels of effort to achieve 30 percent of Technical Recovery Team planning targets, the SIRC 

in spring 2004 voted to use the “ambitious approach,” suggesting a high level of commitment 

by both agencies and individuals. 

• The Stilly-Snohomish Fisheries Enhancement Task Force is successful in attracting a 

substantial number of volunteers to planting and other restoration activities and in providing 

educational programs for schools. 

• Snohomish County SWM took the lead in writing a Centennial Grant proposal that will in 

part provide funds for septic surveys to be conducted by a Snohomish Health District 

registered sanitarian. Snohomish Health District has agreed to be a subcontractor on the 

project and to provide qualified staff for the surveys, and the proposal ranked high on the 

state’s list in January 2005. 

• Snohomish County’s Stillaguamish Steward is experienced and successful in marketing 

restoration projects to private landowners and developing landowner agreements for riparian 

improvements. 

• After a lapse of two years in water quality inspections of dairies in Snohomish County, due 

to transfer of the Dairy Nutrient Management Program from Ecology to Washington State 

Dept of Agriculture, inspections were resumed in fall 2004. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 133

• Snohomish Conservation District (SCD) will continue to provide technical assistance and 

best management practices implementation for Stillaguamish Basin small farms and 

agricultural activities. SCD has proposed a Centennial Grant project (submitted fall 2005; 

likely to receive FY 2006 funding) to provide small farm BMP education in the HarveyKackman-Armstrong and March and Fish Creek sub-watersheds. 

• Whenever applicable BMPs are not being implemented and Ecology has reason to believe 

that individual sites or facilities are causing pollution in violation of RCW 90.48.080, 

Ecology may pursue orders, directives, permits, or enforcement actions to gain compliance 

with the state’s water quality standards. Ecology will enforce water quality regulations under 

Chapter 90.48 RCW. 

Adaptive Management 

Implementation of the Stillaguamish River Watershed TMDL will be adaptively managed such 

that the river’s main stem, Hat Slough, North and South Forks, listed creeks and marine waters 

of Port Susan will meet Washington State’s water quality standards by 2013. Adaptive 

management of the implementation activities and programs could include adjusting best 

management practices, modifying stream sampling frequency and/or locations, conducting 

special inspections in identified source areas, helping develop and fund water quality projects 

that address the pollutant targets of this TMDL, local education initiatives, and other means of 

conforming management measures to current information on the impairment. If water quality 

standards are met without attaining the load allocation reductions specified in this document, 

then the objectives of this TMDL are met and no further reductions are needed. 

One of the more difficult-to-achieve objectives of this TMDL is to make measurable progress in 

reducing the sediment load carried by the Stillaguamish to address the mercury impairments in 

North and South forks. The landslides along North and South forks that contribute excessive 

sediment to this river system have their origins in both natural and anthroporphic processes. As 

Ecology works with local organizations to reduce the impacts of these landslides on the river, 

this agency may need to revisit and redefine this objective in the light of financial and technical 

feasibility of projects to reduce sediment inputs. 

Adaptive management will follow this process: 

(1) The detailed implementation plan (DIP), to be developed by Ecology with review and 

participation of local agencies and organizations, will prioritize locations for addressing 

water quality problems, assign local responsibility, list cleanup activities needed to 

address the problem, and develop a schedule for the activities. 

(2) The detailed implementation plan will also identify locations within the Stillaguamish 

watershed where additional monitoring is needed to identify sources. 

(3) Ecology will facilitate an annual review of water quality data and cleanup activities with 

participation by local organizations and agencies, including Snohomish County Surface 

Water Management, the Stillaguamish and Tulalip Tribes, the city of Arlington, 

Snohomish Conservation District, and other partner watershed organizations. 
Page 134 Stillaguamish Fecal and DO TMDL Submittal Report

(4) Ecology’s tracking of implementation (cleanup) activities will be accomplished through 

this annual review or by individual consultation with the responsible organization. A 

summary spreadsheet will be developed to assist in tracking. This summary spreadsheet 

will be linked to a GIS map tool to locate cleanup activities as appropriate. It is expected 

that some cleanup activities, such as education and outreach programs, will be countywide or watershed-wide and will be tracked only on the spreadsheet. 

(5) Based on the annual review of water quality data and cleanup activities, adjustments will 

be made to the detailed implementation plan (DIP) to ensure that the plan’s sampling 

locations and prioritized cleanup activity list continue to be effective. The updated DIP 

will be made available to local organizations so that their budgeted programs and grant 

applications will reflect any changes in priority locations, priority cleanup actions, and 

identified education and outreach needs. 

(6) Effectiveness monitoring by Ecology is expected to be conducted as soon as 2011 or as 

late as 2013, six to eight years after publication of the detailed implementation plan. The 

decision to schedule effectiveness monitoring will depend on best professional judgment 

that measurable improvement in water quality has occurred, based on the annual review 

of water quality data and implementation tracking,. 

(7) Should implementation occur more quickly, effectiveness monitoring would be 

conducted prior to 2011. 

Table 40. Schedule for Detailed Implementation Plan (DIP) and Adaptive Management 

Task Responsible Organization Target Date 

Pre-DIP review of monitoring 

programs & sample locations 

Ecology with local organizations June 2005 

Pre-DIP review of water quality 

data/Prioritize actions 

Ecology with local organizations August 2005 

Preliminary list of cleanup actions Ecology with local organizations October 2005 

First annual review of water quality 

data/Review & discuss actions 

Ecology with local organizations June 2006 

Detailed Implementation Plan Ecology with local organizations Fall 2006 

Second, 3rd, 4th and 5th annual 

reviews of water quality data/Review 

& discuss actions 

Ecology with local organizations June 2007, 2008, 

2009, 2010 

Effectiveness monitoring Ecology 2011 

Monitoring Strategy 

EPA (1991) guidance calls for a monitoring program for evaluating progress on TMDLs. 

Monitoring is an important tool for assessing the progress or success of implementation 

measures based on the total maximum daily load (TMDL) recommendations. Postimplementation monitoring is required in the TMDL process to ensure that water quality 

standards are being attained and that implementation measures are effective. If water quality 

standards are not met after the TMDL has been established, then adjustments to the load and 

wasteload allocations may be required, or implementation activities may require modification. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 135

Successful TMDL evaluations require several types of monitoring data. Water quality, aquatic 

resources, land use, and implementation activity data are needed to evaluate the progress of the 

TMDL. The details of the location, type, and timing of data collection and TMDL compliance 

schedule will be provided in the detailed implementation plan. 

The following sections provide recommendations and strategies for water quality monitoring and 

implementation activity tracking. 

Recommendations for Monitoring 

 Tributary, mainstem, and Port Susan compliance with fecal coliform standards and reduction 

goals should be measured at the sites where data were used to generate the reduction goals. 

Storm-event data should be included but not over-represented in the record. 

 Intensive monitoring to identify sources and problem reaches are very helpful, but data used 

in those investigations should not be blended with routine monitoring data to determine the 

overall progress of TMDL-related activities. 

 Port Susan fecal coliform data should continue to be collected under the authority of the 

Washington State Department of Health, following the water quality monitoring protocols 

established under the National Shellfish Sanitation Program (NSSP, 2003). 

 Dissolved oxygen data should be collected over day and night cycles during critical periods 

at sites identified as not meeting standards. If multiple samples are not possible, then 

samples should be collected early in the morning close to sunrise to record minimum 

concentrations. 

 Reaches upstream of dissolved oxygen, pH, and fecal coliform monitoring sites should be 

characterized for ground water, wetland, stormwater, and nonpoint source inputs. Reaches 

upstream and downstream of monitoring sites should have salmon and general aquatic habitat 

assessments. 

 Salmon productivity and habitat-limiting factors in Portage, March, Pilchuck, and Kackman 

creeks, as well as Glade Bekken sub-basin, need documentation. 

 Mainstem Stillaguamish River primary productivity response and hyporheic exchange rate 

changes related to seasonal low flows require more spatial and temporal definition. The 

relationships of these physical and biological changes to dissolved oxygen, pH, and nutrients 

need better understanding. 

 Nonpoint sources active during dry or runoff conditions along the mainstem Stillaguamish 

River and its two major forks need to be identified and removed. 

 Stormwater conveyance infrastructures and stormwater quantity and quality need better 

characterization to establish more accurate stormwater load and wasteload allocations. 

• Wastewater treatment plants should include phosphorus and nitrogen monitoring of effluent 

and receiving waters, especially during critical conditions. 

Initial Monitoring Needs 

The detailed implementation plan, to be developed by Ecology with review and participation of 

local agencies and organizations, will prioritize locations for addressing water quality problems, 
Page 136 Stillaguamish Fecal and DO TMDL Submittal Report

assign local responsibility, list cleanup activities needed to address the problem, and develop a 

schedule for the activities. 

Ecology will facilitate an annual review of water quality data and cleanup activities with 

participation by local organizations and agencies, including Snohomish County Surface Water 

Management, the Stillaguamish and Tulalip Tribes, the city of Arlington, Snohomish 

Conservation District, and other partner watershed organizations. The changes in land use and 

the measures used to reduce the impact of land uses on water quality should be inventoried, 

evaluated, and tracked. This will require commitment on the part of partner organizations such 

as Snohomish County because of the extensive effort this could entail. 

Ecology’s tracking of implementation (cleanup) activities will be accomplished through the 

annual review or by individual consultation with the responsible organization. A summary 

spreadsheet will be developed to assist in tracking. This summary spreadsheet will be linked to a 

GIS map tool to locate cleanup activities as appropriate. It is expected that some cleanup 

activities, such as education and outreach programs, will be county-wide or watershed-wide and 

will be tracked only on the spreadsheet. 

Organizations that Monitor Water Quality 

Organizations with capability and experience in monitoring water quality in the Stillaguamish 

watershed include: 

• Snohomish County Surface Water Management 

• Stillaguamish Tribe Natural Resources Department 

• City of Arlington 

• Tulalip Tribes 

• Stilly-Snohomish Fisheries Enhancement Task Force 

• Snohomish Conservation District 

Ongoing water quality monitoring in the basin is conducted by Snohomish County Surface 

Water Management and the Stillaguamish Tribe. Also, Ecology long term river monitoring 

stations are located at: 

• Stillaguamish River near Silvana (05A070 

• South Fork Stillaguamish River at Arlington (05A090) 

• South Fork Stillaguamish River near Granite Falls (05A110) 

• North Fork Stillaguamish River at Cicero (05B070) 

• North Fork Stillaguamish River near Darrington (05B110)
Stillaguamish Fecal and DO TMDL Submittal Report Page 137

Potential Funding Sources 

The Centennial Clean Water Fund, Section 319 grants under the federal Clean Water Act, and 

State Revolving Fund loans are available to fund activities by jurisdictions to help 

implementation of the TMDL. CCWF in spring 2004 awarded the Stillaguamish Tribe funds for 

the Steelhead Haven Landslide Project that will reduce sediment loading and protect the river 

from the shallowing and widening (causing increased exposure to solar radiation) effects of this 

landslide. Additional Salmon Recovery Funds have been awarded to this project. Snohomish 

County, with assistance from the Snohomish Health District, applied in fall 2004 for Centennial 

Funds for the Snohomish County Septic Systems project, which would include pilot projects in 

two sub watersheds of the Stillaguamish. Non-governmental organizations can apply for 319 

grant funding. Should additional funding be necessary to reach standards, Ecology will work 

with the local organizations to prepare appropriate scopes of work, to implement this TMDL, and 

to assist with applying for grant opportunities as they arise. 

Grants through Ecology’s Centennial Clean Water Fund, Section 319, and State Revolving Fund 

loans continue to provide resources to fund implementation activities identified in the TMDL. 

The Puget Sound Water Quality Action Team administers Public Involvement and Education 

grants. The Conservation District provides technical assistance and BMP cost-sharing funding 

using local (Clean Water District), state and federal funds, as available. The Stillaguamish Tribe 

and the conservation district write CREP plans and work with landowners to get riparian buffers 

installed with funds from the Farm Service Agency and the Washington Conservation 

Commission. The federal Natural Resources Conservation Service provides some technical 

assistance and also administers the Environmental Quality Incentive Program (EQIP), which 

provides cost share funds for BMPs on agricultural sites. Stream restoration activities are 

eligible for salmon restoration grants through various sources. 

The Lower Stillaguamish Clean Water District is supported through a fee assessment on property 

owners in the lower part of the watershed for projects related to drainage and improved water 

quality in Port Susan for shellfish and fish. Besides the portion administered by Snohomish 

County Surface Water Management for drainage and other improvement projects, some Clean 

Water District fees go to Snohomish Conservation District (above paragraph); also a 

Discretionary Fund of approximately $45,000 is available annually for on-the-ground projects to 

improve water quality and aquatic habitat. The Clean Water District Citizens Advisory Board is 

charged with reviewing grant applications for these funds. 
Page 138 Stillaguamish Fecal and DO TMDL Submittal Report

References Cited 

APHA et al., 1998. Standard Methods for the Examination of Water and Wastewater. 

Twentieth edition. American Public Health Association, American Water Works Association, 

and Water Pollution Control Federation. Washington D.C. 

Aroner, E., 1995. WQHYDRO: Water Quality/Hydrology/Graphics and Analysis System. 

Portland, OR. 

ASAE, 1998. Manure Production and Characteristics. Standard ASAE D384.1 DEC99. 

American Society of Agricultural Engineers, St. Joseph, MI. 

Bailey, G., 2002. Permit Writer’s Manual. Revised July 2002. Washington State Department 

of Ecology, Water Quality Programs, Olympia, WA Publication 92-109. 

http://www.ecy.wa.gov/biblio/92109.html. 

Barlond, O., 2001. Photographs and notes on flooding in the Portage Creek sub-basin in 2000 

and 2001. Email digital photographs sent on various dates. 

Biggs, B.J.F., 2000. Eutrophication of streams and rivers: dissolved nutrient-chlorophyll 

relationships for benthic algae. Journal North American Benthological Society 19(1):17-31. 

Blake, B., 2002. Personal communication. City of Arlington, Arlington, WA. 

Calambokidis, J., B.D. McLaughlin, and G.H. Steiger, 1989. Bacterial Contamination Related 

to Harbor Seals in Puget Sound, Washington. Cascadia Research Collective report to Jefferson 

County and Washington State Department of Ecology, Olympia, WA. 74 pgs. 

Canaan, J. 2004. Personal communication (email) from Jeff Canaan, WSDA Livestock Nutrient 

Management Program, regarding water quality inspections of livestock facilities in Snohomish 

County, Oct. 1, 2004, with S. Lawrence, Ecology Northwest Regional Office. 

Chapra, S.C., 1997. Surface Water Quality Modeling. McGraw-Hill Companies, Inc. 

Chapra, S.C., 2001. Water-Quality Modeling Workshop for TMDLs, Washington State 

Department of Ecology, Olympia, WA, June 25-28, 2001. 

Connolly, P.J., 2001. Stillaguamish River Watershed Restoration. 1999 Annual Report. Edited 

by P.J. Connolly, U.S. Geological Survey, Columbia River Research Laboratory, Cook, WA. 

Prepared for Bonneville Power Administration, Environment, Fish and Wildlife, Portland, OR, 

Project Number: 1998-019-01. 

Cullinan, T., 2001. Important Bird Areas of Washington. Washington Audubon and 

Washington Department of Fish and Wildlife, Olympia, WA. 

Cusimano, R., 1997. Water Quality Assessment of Tributaries to the Snohomish River and 

Nonpoint Source Pollution TMDL Study. Washington State Department of Ecology, Olympia, 

WA. Publication No. 97-334. 52 pgs. http://www.ecy.wa.gov/biblio/97334.html
Stillaguamish Fecal and DO TMDL Submittal Report Page 139

DNR (Washington State Department of Natural Resources). 1999. Forests and Fish Report, 

April 29, 1999: Report to the Forest Practices Board and the Governor’s Salmon Recovery 

Office by DNR, Ecology, representatives of Tribes, and federal agencies. 

Dodds, W.K. and E.B. Welch, 2000. Establishing nutrient criteria in streams. Journal of the 

North American Benthological Society 19(1):186-196. 

Earth Tech, 1997. City of Arlington Stillaguamish River Water Quality Monitoring Report. 

Prepared for the City of Arlington by Earth Tech Consultants. December 1997. Bellevue, WA. 

24 pgs. + appendices. 

Ecology, August 2004. Data Summary: Stillaguamish River watershed fecal coliform, dissolved 

oxygen, pH, mercury and arsenic Total Maximum Daily Load study. Joe Joy, Sarah Coffler, and 

Kimberly Gridley. Washington State Department of Ecology, Environmental Assessment 

Program, Olympia, WA. Publication No. 04-03-037. 

Ecology, July 2004. Stillaguamish River Watershed Fecal Coliform, Dissolved Oxygen, pH, 

Mercury and Arsenic Total Maximum Daily Load Study. Joe Joy, Washington State Department 

of Ecology, Environmental Assessment Program, Olympia, WA. Publication No. 04-03-017. 

http://www.ecy.wa.gov/biblio/0403017.html

Ecology, March 2004. Stillaguamish River Watershed Temperature Total Maximum Daily Load 

Study. Greg Pelletier, Washington State Department of Ecology, Environmental Assessment 

Program, Olympia, WA. Publication No. 04-03-010. 

http://www.ecy.wa.gov/biblio/0403010.html. 

Ecology, 2003a. Ecology Environmental Information Management System data. Washington 

State Department of Ecology, Olympia, WA. 

Ecology, 2003b. http://www.ecy.wa.gov/programs/eap/models/

Ecology, 2002. Proposed Chapter 173-201A. December 19, 2002. Washington State 

Department of Ecology, Olympia, WA. http://www.ecy.wa.gov/programs/wq/swqs/rev_rule.html

Ecology. 2001. Stillaguamish River Basin and Port Susan Total Maximum Daily Load 

Evaluation Update: Quality Assurance Project Plan. Joe Joy, Washington State Department of 

Ecology, Environmental Assessment Program, Olympia, WA. December 2001. Publication No. 

01-03-065. 61 pgs. http://www.ecy.wa.gov/biblio/0103065.html

Ecology, 2001. Stillaguamish River Temperature Total Maximum Daily Load: Quality 

Assurance Project Plan. Greg Pelletier and Dustin Bilhimer, Environmental Assessment 

Program, July 30, 2001. 

Ecology, 2001. Stormwater Management Manual for Western Washington, Washington State 

Department of Ecology, Water Quality Program, Olympia, WA, August 2001. 

Ecology, 2000. Final 1998 Section 303(d) List – WRIA 5 Data Decision Matrix. Washington 

State Department of Ecology, Water Quality Program, Olympia, WA. 
Page 140 Stillaguamish Fecal and DO TMDL Submittal Report

Ecology, 2000. Washington's Water Quality Management Plan to Control Nonpoint Source 

Pollution, Washington State Department of Ecology, Water Quality Program, Olympia, WA 

98504-7710, June. 2000. 

Ecology, 1998. Setting standards for the bacteriological quality of Washington’s surface waters 

– preliminary review draft discussion paper, January 1998. Washington State Department of 

Ecology, Water Quality Program, Olympia, WA. 32 pgs. 

Ecology, 1994. Watershed Approach to Water Quality Management: Needs Assessment for 

Skagit/Stillaguamish Watershed. June 1994. Prepared by S. Messman, G. Dorf, B. Duffy; 

Northwest Regional Office Water Quality Program. 

Embrey, S., 2001. Microbiological quality of Puget Sound basin streams and identification of 

contaminant sources. Journal of the American Water Resources Association 37(2): 407-421. 

EPA, 2000. Ambient Water Quality Criteria Recommendations Information supporting the 

development of State and Tribal nutrient criteria: Rivers and Streams in Nutrient Ecoregion II. 

EPA 822-B-00-015 December 2000. U.S. Environmental Protection Agency, Office of Water, 

Washington, D.C. 

EPA, 2001. Protocol for Developing Pathogen TMDLs, U. S. Environmental Protection Agency, 

EPA 841-R-00-002, Washington, D. C., 90 pp. and appendices. 

EPA, 1999. National Recommended Water Quality Criteria – Corrected. U.S. Environmental 

Protection Agency, Office of Water, Washington, D.C. EPA 882-Z-99-001. 

EPA, 1998. Report of the Federal Advisory Committee on the Total Maximum Daily Load 

(TMDL) Program. The National Advisory Council for Environmental Policy and Technology 

(NACEPT). U.S. Environmental Protection Agency, Office of the Administrator. EPA 100-R98-006. 

EPA, 1997. Memorandum of Agreement Between the USEPA and Washington State Department 

of Ecology Regarding the Implementation of Section 303(d) of the Federal Clean Water Act, U. 

S. Environmental Protection Agency, 1997, 22 pp. 

EPA, 1991. Guidance for Water Quality-based Decisions: The TMDL Process. 

U.S. Environmental Protection Agency. EPA 440/4-91-001. 

EPA, 1986. Quality Criteria for Water. U.S. Environmental Protection Agency, Office of 

Water, Washington, D.C. EPA 440/5-86-001. 

Erkenbrecher, Jr., C.W., 1981. Sediment bacterial indicators in an urban shellfishing subestuary 

of the lower Chesapeake Bay. Applied and Environmental Microbiology 42(3):484-492. 

Gilbert, R.O., 1987. Statistical Methods for Environmental Pollution Monitoring. Van Nostrand 

Reinhold Company, New York, NY. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 141

Huber, H., 2003. Personal communication. National Marine Fisheries Service. 

Huntting, M.T., 1956. Inventory of Washington Minerals: Part II Metallic Minerals, Volume 2 -

– Maps. Bulletin No. 37. Washington State Department of Conservation and Development, 

Division of Mines and Geology, Olympia, WA. 

Jezorek, I. and P.J. Connolly, 2001. Stillaguamish River Watershed Project 1999 Annual Report, 

Report H: Flow, Temperature, and Habitat Conditions in the Stillaguamish River Watershed. 

USGS Columbia River Research Laboratory, Cook, WA. 

Johnson, A., 2002. Results and Recommendations from Monitoring Arsenic Levels in 

303(d)-listed Rivers in Washington. Washington State Department of Ecology, Olympia, WA. 

Publication No. 02-03-045. 20 pgs. http://www.ecy.wa.gov/biblio/0203045.html

Joy, J. and N. Glenn, 2000. Stillaguamish River Basin Pre-TMDL Assessment. March 2000, 

unpublished. Washington State Department of Ecology, Olympia, WA. 8 pgs. + figures 

 

Kitsap County Health District. 2004. Dogfish Creek Final Report. 27 pp. 

http://www.kitsapcountyhealth.com/environmenta_health/water_quality/docs/MonotoringReport

Docs/2004_report_dogfish_creek.pdf

Klopfer, D., 2000. Unpublished data collected by the Stillaguamish Tribe, Arlington, WA. 

Presented in Everett, WA. 

Klopfer, D., 2002. Personal communication. Stillaguamish Tribe, Arlington, WA. 

Knight, K. 2004. Personal communication (email) to S. Lawrence, Washington Dept. of 

Ecology, Oct. 22, 2004. Kris Knight, Restoration Site Supervisor, The BankSavers Project, 

Stillaguamish Tribe, Arlington, WA. 

McKay, Jr., D., D.K. Norman, M.A. Shawver, and R.F. Teissere, 2001. Directory of Mines, 

2001. Washington State Department of Natural Resources, Division of Geology and Earth 

Resources, Olympia , WA. Information Circular 94. August 2001. 

Naegeli, M.W. and U. Uehlinger, 1997. Contribution of the hyporheic zone to ecosystem 

metabolism in a pre-alpine gravel-bed river. Journal of North American Benthological Society

16 (4): 794-804. 

National Shellfish Sanitation Program. 2003. Guide to Control of Molluscan Shellfish. 

www.cfsan.fda.gov/~ear/nss2-toc.html 

National Stormwater Quality Database, 2004. Phase I NPDES MS4 monitoring database 

established by Robert Pitt, Alex Maestre, and Renee Morquecho of the University of Alabama. 

http://unix.eng.ua.edu/~rpitt/Research/ms4/mainms4.shtml 

Norman, D.K., 2000. Washington’s Inactive and Abandoned Metal Mine Inventory and 

Database. Washington Geology, 28:1/2. September 2000. Pgs. 16-18. 
Page 142 Stillaguamish Fecal and DO TMDL Submittal Report

Novotny, V. and H. Olem, 1994. Water Quality Prevention, Identification, and Management of 

Diffuse Pollution. Van Nostrand Reinhold, New York, NY. 

Ott, W., 1995. Environmental Statistics and Data Analysis. Lewis Publishers, New York, NY. 

Paulsen, K., K. Thornburgh, and K. Rawson, 1991. Stillaguamish River Volunteer Water 

Quality Monitoring Project. Tulalip Tribes Fisheries Department, Progress Report No. 91-4. 

Marysville, WA. 

Pelletier G. and S. Chapra, 2003. QUAL2Kw – Documentation and user manual for a modeling 

framework to simulate stream water quality. Draft 4-September 2003. Washington State 

Department of Ecology, Olympia, WA. 138 pgs. 

Pelletier, G. and D. Bilhimer, 2001. Quality Assurance Project Plan: Stillaguamish River 

Temperature Total Maximum Daily Load. Washington State Department of Ecology, 

Olympia WA. 

Plotnikoff, R., 1991. Portage Creek: Nonpoint Source Pollution Effects on Quality of the Water 

Source. Publication No. 95-300. Washington State Department of Ecology, Olympia, WA. 94 

pgs. 

Puget Sound Water Quality Action Team, 1998. 1998 Puget Sound Update: Sixth Report of the 

Puget Sound Ambient Monitoring Program. Olympia, WA. 

Raforth, R.L., D.K. Norman, and A. Johnson, 2002. Second Screening Investigation of Water 

and Sediment Quality of Creeks in Ten Washington Mining Districts, with Emphasis on Metals. 

Washington State Department of Ecology, Olympia, WA. Publication No. 02-03-024. 94 pgs. 

http://www.ecy.wa.gov/biblio/0203024.html. 

Randolph, D., 2000. Personal communication. City of Arlington, Arlington, WA. 

Sargeant, D., 2002. Dungeness River and Matriotti Creek Fecal Coliform Bacteria Total 

Maximum Daily Load Study. Washington State Department of Ecology, Olympia, WA. 

Publication No. 02-03-014. 46 pgs. http://www.ecy.wa.gov/biblio/0203014.html

SIRC. 2004. Draft Chinook Salmon Recovery Plan for Stillaguamish Watershed – WRIA 5. 

June 30, 2004. Prepared by Jones & Stokes, Bellevue, WA for Stillaguamish Implementation 

Review Committee (SIRC) and Puget Sound Shared Strategy 

Snohomish County, 2002. NPDES Municipal Stormwater Discharge Permit 2001 Annual 

Report. Snohomish County Public Works, Surface Water Management Division, Everett, WA. 

59 pgs. 

Snohomish County Health District and Washington State Department of Health, 1991. Seasonal 

Study of Arsenic in Ground Water, Snohomish County. Washington State Department of Health, 

Environmental Health Programs, Office of Toxic Substances, Olympia, WA. 40 pgs. 
Stillaguamish Fecal and DO TMDL Submittal Report Page 143

Stienbarger, D., 1995. Inventory and Evaluation of Livestock Operations and the Potential for 

Non-point Pollution in the Stillaguamish Clean Water District. Snohomish Conservation 

District, Everett, WA. 26 pgs. 

Stormwater Center, 2004. Simple Method to Calculate Urban Stormwater Loads. 

http://www.stormwatercenter.net. Go to “Monitor/Assess.” Select “Rapid Assessment Methods” 

to get to Simple Method. 4 pgs + tables. 

Thomann, R.V. and J.A. Mueller, 1987. Principles of Surface Water Quality Modeling and 

Control. Harper and Row, New York, NY. 

Thomas, B.E., J.M. Wilkinson, and S.S. Embrey, 1997. The Ground-water System and 

Ground-water Quality in Western Snohomish County, Washington. U.S. Geological Survey 

Water-Resources Investigations Report 96-4312. Tacoma, WA. 218 pgs. 

Thornburgh, K. 2004. Personal communication (email) from Kathy Thornburgh, Snohomish 

County Surface Water Management Biologist regarding Snohomish County Centennial Grant 

proposal, “Snohomish County Septic Systems,” September 2, 2004, with S. Lawrence, Ecology 

Northwest Regional Office. 

Thornburgh, 2001. Glade Bekken Watershed Restoration and Monitoring. Snohomish County 

Public Works, Surface Water Management Program, Everett, WA. 34 pgs 

Thornburgh and Williams, 2001. State of the Waters, 2000: Water Quality in Snohomish 

County’s Rivers, Streams, and Lakes. Snohomish County Public Works, Surface Water 

Management Program, Everett, WA. 

TMDL Workgroup, 1997. Total Maximum Daily Load Development Guidelines. Washington 

State Department of Ecology, Environmental Assessment Program, Olympia, WA. Publication 

No. 97-315. 30 pgs. http://www.ecy.wa.gov/biblio/97315.html

Uehlinger, U., 2000. Resistance and resilience of ecosystem metabolism in a flood-prone river 

system. Freshwater Biology 45: 319-332. 

USDA Forest Service and USDI Bureau of Land Management. 1994. Record of Decision for 

Amendments to Forest Service and Bureau of Land Management Planning Documents within the 

Range of the Northern Spotted Owl. Portland, Oregon. 73p. 

USFDA, 2000. National Shellfish Sanitation Program Model Ordinance. U.S. Food and Drug 

Administration Center for Food Safety and Applied Nutrition, Office of Seafood. 1999 Revision 

released November 3, 2000. Washington, D.C. http://www.cfsan.fda.gov/~ear/nsspotoc.html

USGS, 1997. The ground-water system and ground-water quality in western Snohomish County, 

Washington. U.S. Geological Survey, Water Resources Investigations Report 96-4312, Tacoma, 

WA. 
Page 144 Stillaguamish Fecal and DO TMDL Submittal Report

Vervier, P. and R.J. Naiman, 1992. Spatial and temporal fluctuations of dissolved organic 

carbon in subsurface flow of the Stillaguamish River (Washington, USA). Archives 

Hydrobiologie 123(4): 401-412. 

Warren, C.E., 1971. Biology and Water Pollution Control. W.B. Saunders Company. 

Philadelphia, PA. 

Washington State Office of Financial Management, 2003. 2003 Population Trends for 

Washington State, September 2003, Olympia, WA. 

Wayland, R.H. and J.A. Hanlon, 2002. Establishing Total Maximum Daily Load (TMDL) 

Wasteload Allocations (WLAs) for Storm Water Sources and NPDES Permit Requirements 

Based on those WLAs, U. S. EPA, Office of Water, Memorandum to Water Directors EPA 

Regions 1 – 10, Washington, D.C., November 22, 2002, 6 pp. 

WCC, 1999. Salmon and Steelhead Habitat Limiting Factors Water Resource Inventory Area 5, 

Stillaguamish Watershed. Washington State Conservation Commission, Olympia, WA. 

Weiskel, P.K., B.L. Howes, and G.R. Heufelder, 1996. Coliform contamination of a coastal 

embayment: sources and transport pathways. Environmental Science and Technology 30, 

6:1872-1881. 

West, J., S. O’Neill, G. Lippert, and S. Quinnell, 2001. Toxic Contaminants in Marine and 

Anadromous Fishes from Puget Sound, Washington. Washington Department of Fish and 

Wildlife, Olympia, WA. 311 pgs. 
Stillaguamish Fecal and DO TMDL Submittal Report Page A-145 

Appendix A. 

Public Participation Including 

 Responses to Comments
Page A-146 Stillaguamish Fecal and DO TMDL Submittal Report
Stillaguamish Fecal and DO TMDL Submittal Report Page A-147 

Public Participation 

In 2000 through 2004, Ecology developed TMDLs for fecal coliform bacteria, dissolved oxygen 

and temperature in the Stillaguamish watershed. (A chronology is provided below.) Data 

collection and analysis benefited greatly from suggestions and interpretation from local 

watershed participants. The final TMDL studies include water quality data provided by the 

Stillaguamish Tribe and Snohomish County Surface Water Management, among others. During 

writing of the TMDL studies, Ecology water quality scientists and the TMDL lead presented 

results and recommendations for implementation to local organizations, Tribes and government 

agencies at a number of meetings at TMDL meetings convened by Ecology in the watershed. 

Watershed residents have learned about the TMDL water cleanup plans in other ways. News 

releases were issued by Ecology’s Northwest Regional Office when the temperature TMDL 

study was published in March and when the fecal coliform bacteria, dissolved oxygen, pH, 

mercury, and arsenic TMDL study was published in July 2004. The latter news release led to an 

article by reporter Christopher Schwarzen, “Bacteria, other pollutants in Stillaguamish targeted,” 

in the Snohomish County edition, Seattle Times, on September 8, 2004. 

The draft TMDL summary implementation strategy was presented at a public meeting in 

Arlington on November 9, 2004, from 4 to 8 p.m. The public comment period on the draft, 

which was posted on Ecology’s WRIA 5 TMDL website, extended from November 3 to 

December 17, 2004 to allow for public and local agency review and feedback. Public notice for 

the commencement of the public comment period and public meeting consisted of a mailed 

Focus Sheet and legal advertisement in the Arlington and Everett newspapers on November 3, 

2004. 

Ecology’s responses to comments are provided in this appendix following the chronology of 

TMDL development. 

Chronology of Non-Point Water Quality Planning and TMDLs for the 

Stillaguamish Watershed 

Development of the Stillaguamish TMDL for fecal coliform bacteria, dissolved oxygen, pH, 

arsenic and mercury, and the second TMDL for temperature, have their early origins in the 

Stillaguamish Watershed Action Plan (January 1990). This “Nonpoint Action Plan” was 

developed under WAC 400-12 under a Centennial Fund grant to Snohomish County. To provide 

for strong public involvement in development of the watershed plan, a Citizens Advisory 

Committee (CAC) was formed. This CAC has continued its commitment to watershed planning 

and improvement. Now, renamed the Stillaguamish Implementation Review Committee (SIRC), 

the committee is the lead entity for salmon restoration planning in the watershed and has 

continued to provide strong support for and coordination of water quality improvements. 

Ecology’s TMDL process in the Stillaguamish includes the milestones listed below, followed by 

approximate dates for completing the TMDL in 2005 through 2007. 
Page A-148 Stillaguamish Fecal and DO TMDL Submittal Report

June 1994—Ecology Water Quality Needs Assessment for Skagit/Samish/Stillaguamish 

Watersheds identified a “Lower Stillaguamish & Portage Creek TMDL for DO, turbidity and 

FC” as a medium priority future project (Ecology 1994). 

March 2000—Pre-TMDL Assessment completed. 

2001—Quality Assurance Project Plans completed for Temperature TMDL study (July) and for 

Fecal Coliform, Dissolved Oxygen, pH, Arsenic and Mercury TMDL study (December). 

June 2000 – June 2002—Data for TMDLs based on water quality sampling by Ecology with 

additional data provided by the Stillaguamish Tribe and Snohomish County Surface Water 

Management. Airplane-based aerial surveys of Stillaguamish Watershed for infrared sensing of 

water temperature took place on September 7 and 8, 2001. 

2003 and 2004—Analysis of TMDL data. Computer models were used to evaluate loadings 

affecting dissolved oxygen conditions in river under critical low flow condition; also to model 

effects of changes in riparian vegetation, water withdrawals, channel width changes and riparian 

microclimate changes on stream temperature under critical low flow conditions. 

November 2003—Ecology reviewed a directive by EPA to include estimates of stormwater 

contributions in TMDLs and assign Wasteload Allocations to current and future NPDES 

stormwater permittees (Snohomish County; City of Arlington; and Washington State Department 

of Transportation.) 

2003 and 2004—Watershed meetings on progress of the TMDL study. 

November 4, 2004—Draft Summary Implementation Strategy distributed by email to watershed 

advisory group, local agencies, Tribes and made available online at Ecology’s WRIA 5 TMDL 

website. 

November 9, 2004—Public meeting on Draft TMDL Summary Implementation Strategy. 

December 17, 2004—Public comment period closed. 

February 2005—TMDL Summary Implementation Strategy to be submitted to EPA for 

approval. 

2005 - 2007—TMDL Detailed Implementation Plan to be developed by Ecology with watershed 

organizations. 
Stillaguamish Fecal and DO TMDL Submittal Report Page A-149 

From: Altose, Larry 

Sent: Thursday, December 09, 2004 6:15 PM 

To: Lawrence, Sally (ECY); Hirschey, Steve 

Cc: Garland, Dave; Palenshus, DouGlas; Beitel, Judy; Swenson, Dan 

Subject: News; Stanwood-Camano News; 11-2-04; Stilly 

_________________________________ 

Larry Altose, Public Information 

Wash. Dept. of Ecology, NW Region 

425-649-7009
Page A-150 Stillaguamish Fecal and DO TMDL Submittal Report

Response to Comments 

Comments received during the public review period November 9 – December 17, 2004, are 

paraphrased below followed by Ecology’s responses. Many comments were addressed by 

adopting recommended text changes in this submittal report; those that were not are included 

here. Responses to comments on the In Stream Flow Rule Presentation for the Stillaguamish 

River were provided by Ecology Northwest Regional Office’s Water Resources Program. 

Comment. Recommendations in the plan that discuss pollutants other than bacteria, dissolved 

oxygen, or temperature, or any recommendations that discuss nutrients, are inappropriate. 

Response: Temperature, fecal coliform, and dissolved oxygen were the major pollutants 

evaluated in the Stillaguamish River Watershed TMDL studies. However, nutrients, pH, arsenic, 

mercury, suspended sediment, channel structure, riparian conditions, and instream flows were all 

discussed in the studies. Nutrients, including load allocations, were specifically discussed in 

relation to dissolved oxygen and pH conditions in the Stillaguamish River mainstem and its two 

major forks in the conventional contaminants report. Suspended sediment reductions were 

recommended to reduce mercury and arsenic concentrations in the convention contaminants 

report, and to reduce temperatures from channel filling and bank erosion (channel widening) 

effects in the temperature report. 

Comment: Reference to nutrients associated with septic waste is extraneous to discussion. 

Reference to ground water depleting oxygen in surface waters should also explain that this is a 

natural condition and not subject to remediation or load allocations. 

Response: The sentence may require a bit more elaboration, but it is not extraneous to the 

discussion. The reference to nutrients from poorly maintained or constructed on-site septic 

system waste relates to the set of bullets on the previous page where the potential relationship 

between nutrients and low dissolved oxygen conditions is mentioned. We agree that it would be 

correct to mention that ground water with depressed oxygen would not require remediation; 

however, it would be included as a background load that could influence other wasteload or load 

allocations to the water body. 

Comment: References to sediment as a pollutant in the TMDL are not appropriate. 

Response: This fecal coliform and dissolved oxygen TMDL addresses arsenic and mercury in 

the watershed as well as fecal coliform bacteria, pH and dissolved oxygen. The analysis 

demonstrated that arsenic and mercury tend to be associated with sediment particles. Measures 

that reduce the overall sediment load in the river are recommended for their effect in reducing 

arsenic and mercury as well. 

Comment: We feel that it is inappropriate to include any recommendations that discuss nutrients 

in the plan. Remove references to pollutants not specifically addressed in this TMDL. 

Response: The response to Comment 1 applies to this comment as well. Nutrient controls were 

addressed in the conventional contaminants report to control depressed dissolved oxygen and 
Stillaguamish Fecal and DO TMDL Submittal Report Page A-151 

elevated pH in parts of the watershed. Phosphorus load allocations were set for the North Fork 

Stillaguamish River to control pH. Recommendations were also made in this report to conduct 

additional nutrient input characterizations in the lower North Fork and South Fork and in the 

confluence reach downstream to the Interstate 5 Bridge. The seasonal dissolved oxygen 

depression in that reach is thought to be influenced by nutrient loads. The implementation 

strategy could name these areas specifically, but it would be reasonable management 

recommendation for Snohomish County to characterize nutrients in stormwater discharged to 

other water bodies as well. 

Comment: Is the prevalence of beaver dams considered when setting load allocations for BOD 

to improve dissolved oxygen levels? Do we know how beaver dams affect DO and BOD? 

Response: Ecology did not investigate the relationship of beavers to stream oxygen 

concentrations. To investigate this, one would need to look at the effects of their biological BOD 

output as well as the effects of their hydrological modifications on the stream that would tend to 

increase re-aeration over the dam and settle out organic particulates commonly associated with 

BOD in the pool behind the dam. 

Comment: Kackman Creek is crossed by 252nd Street NE at two locations approximately 1500 

feet apart. Which was the sampling location? 

Response: The sampling location is on the N (upstream) side of the road where the creek crosses 

a second time (the eastern of the two crossings). 

Comment: The TMDL addresses only problems associated with low flows and salmon, and 

ignores problems associated with high flows. 

Response: The TMDL includes an analysis of the seasonal variation and critical conditions 

associated with periods of more frequent or higher exceedances of water quality standards. Fecal 

coliform bacteria problems in some of the parts of the watershed were more prevalent during the 

wet season, when flows are higher. As a result, wasteload allocations were developed for Phase 

I NPDES municipal stormwater permittees (Snohomish County and WSDTOT) and for future 

Phase II stormwater permittee City of Arlington. Typical best management practices to reduce 

bacteria are those that infiltrate stormwater or delay and dampen storm flows by using 

stormwater detention ponds, which have the additional beneficial effect of settling out particles 

that bacteria may be associated with. 

Comment: Stanwood WWTP is not assigned any Waste Load Allocations. 

Response: Stanwood WWTP and other discharges to the Old Stillaguamish Channel will be 

evaluated in a future Old Stillaguamish Channel TMDL. 

Comment: The percentages in “Estimated portions of FC Load” column in Table 35 total to 

136.8% and we assume this allows for some loss to die-off and deposition so that it totals (with 

point and background loads) 100 percent of the total load that may be delivered to Port Susan (or 

other limiting location). 
Page A-152 Stillaguamish Fecal and DO TMDL Submittal Report

Response: This column of percentages is not intended to be summed and therefore do not add 

up to 100 percent. Wasteload allocations were assigned at all sampling locations in the 

watershed where: 

• The reach required fecal coliform reductions in order to meet standards. 

• The reach receives stormwater drainage from a Phase I or future Phase II stormwater 

permittee. 

For each of these reaches, the amount of roadway area and/or adjacent land that would drain to 

each location was estimated using topographic information. Estimates of the amount of fecal 

coliform characteristic of roadways and other land uses were developed using a national 

stormwater database, as explained in Appendix C (the Simple Method). For example, a small 

percentage (5 percent) of the FC Load is assigned to Snohomish County for Fish Creek in Table 

35 based on the runoff and the associated FC load for roadways up-drainage from the site. The 

remaining 95 percent of the load at this site is estimated to be from non-point sources, not from 

other point sources. 

Comment: The “Wasteload Allocations” assigned in Table 35 require discharge estimates to 

calculate loads. Ecology needs to inform stormwater permittees of appropriate methods for 

measurement of discharge and concentrations in order to calculate loads. This permittee 

questions whether the WLAs can be attained even if discharges had modest concentrations and 

low flow. 

Response: Ecology will work with, and review the proposals of, all stormwater permittees as 

they develop approaches for addressing the wasteload allocations. The development of the 

detailed implementation plan is an opportunity for permittees to propose stormwater monitoring 

and/or stormwater BMPs with rationale for their appropriateness for particular discharge 

locations. 

Comment: The Simple Method estimates stormwater runoff pollutant loads from small urban 

areas and is not the right model for characterizing larger urban and non-urban areas. A more 

sophisticated model such as HSPF may be needed to analyze a large and complex watershed like 

the Stillaguamish. 

Response: We recognize that the Simple Method model does not provide as accurate of a 

stormwater loading characterization as one would expect from a continuous simulation model 

like HSPF. As explained on pages 28 and 100 of the report, stormwater loading quantification 

for wasteload allocations (WLAs) was an additional task placed upon the Stillaguamish TMDL 

evaluation by the USEPA after the monitoring study was completed. The USEPA directive does 

‘recognize that these allocations might be fairly rudimentary because of data limitations and 

variability in the system’ (Wayland and Hanlon, 2002). 

We believe that the Simple Method model addresses quantification of stormwater loads at a 

‘screening level’ scale commensurate with the data currently available in the basin. The model is 

recommended by the USEPA as providing a ‘quick and reasonable estimate of pollutant 

loadings’ (USEPA, 1992). The model is a set of simple annual or seasonal pollutant loading 

equations that is a basic unit loading approach used for modeling urban or rural environments; 

many pollutant wash-off models of varying spatial scales are similarly constructed. Since the 
Stillaguamish Fecal and DO TMDL Submittal Report Page A-153 

numeric results do not go into the NPDES permit, the model ‘loads’ are only meant to suggest 

relative magnitude from various land use types – not necessarily a highly accurate accounting of 

loads. 

In all but two cases, ‘Roadway’ loads assigned to WSDOT and Snohomish County are less than 

10 percent of the cumulative fecal coliform loads in most tributaries. These numbers do not 

appear to be outside of what might be expected, especially in a rural area where manure hauling 

takes place, and discarded diapers are frequently found along the roadways. Drainages from 

adjacent properties into the permit holder’s infrastructure are not closely managed and could be 

contributing loads as well. 

The NPDES permit will only list best management practices (BMPs) that will likely reduce the 

pollutant loads. WSDOT may already have BMPs in place on the drainage systems discharging 

to the listed water bodies in the Stillaguamish basin. These BMPs can be listed in the TMDL 

detailed implementation plan that will be written over the coming year. By listing these 

treatment practices and by better characterizing the potential impact of stormwater from WSDOT 

highways and facilities in future monitoring work, we can more accurately determine the 

pollutant loads. 

Comment: The impervious cover for Interstate 5 (80%) is overestimated since the area counted 

as roadway includes vegetated right-of-way – this makes WSDOT highways in the Stillaguamish 

watershed more rural in nature. The majority of the stormwater runoff in the Stillaguamish 

watershed is generated as sheet flow that infiltrates to ground water rather than surface runoff. 

Response: The impervious cover and runoff factor were purposefully set at the relatively high 

default values recommended in the model. TMDL evaluation protocols require conservative 

assumptions for margin of safety considerations, especially in cases where data specific to the 

source are absent. We used this conservative assumption since we did not receive specific 

information about the nature of the highway stormwater drainage systems in the Stillaguamish 

basin. We found aWSDOT geographical information system (GIS) coverage of outfall locations 

on Interstate 5 and major highways in the Stillaguamish basin, but information from WSDOT 

about the kind of treatment systems in place at these outfall, though requested, was not provided. 

On the other hand, we did not include potential pollutant discharges from adjacent land uses even 

though some may be entering the WSDOT stormwater systems. We made a conscious decision 

not to stack too many conservative assumptions in the analysis. 

 

Comment: The conveyance of pollutant loads to roadside ditches from adjacent land uses could 

be of greater significance than the contribution of the roadways themselves. 

Response: We agree. As noted in the previous two responses, this could well be the case and 

conservative coefficients were used to account for such loads. Unfortunately WSDOT, 

Snohomish County, and other jurisdictions under the stormwater permit system are responsible 

for these pollutant loads because they manage the conveyance system. It is up to the owner of 

the conveyance to ensure that pollutant loads from adjacent land uses are adequately treated. 

Comment: WSDOT is concerned with the process of assigning a wasteload allocation (WLA) 

based solely on NPDES permits for stormwater systems, particularly when there are no data to 
Page A-154 Stillaguamish Fecal and DO TMDL Submittal Report

confirm the WLA. In rural jurisdictions with few or no permit holders other than WSDOT, and 

an inadequate data set to characterize nonpoint sources for load allocation, a WLA does not 

appear justified. 

Response: The TMDL evaluation attempts to use the best available data to address the potential 

sources of pollutants. The Stillaguamish River basin TMDL assigned estimated load allocations 

to both point and nonpoint sources as required by law. In almost every tributary system 

evaluated, nonpoint source load allocations were greater than point source wasteload allocations. 

The TMDL evaluation suggests that nonpoint sources will require more implementation work 

and greater pollutant reductions than the point sources to reduce pollutant loads in the basin. 

This would be expected in a rural basin. 

Comment: The Stormwater Management Manual for Western Washington (Ecology 

Publications 99-11 through 99-15) does not provide any best management practices that are 

designed for reduction of fecal coliform, nor does the 2004 Highway Runoff Manual. Will 

Ecology be establishing reductions in the fecal coliform WLA for WSDOT? If so, in order for 

Ecology to set meaningful goals for reducing fecal coliform in stormwater discharges, it will first 

need to establish a means of meeting those goals. 

Response: Though the stormwater management manuals don’t have BMPs that are specifically 

designed to reduce bacterial loads, some of the BMPs are more capable of doing so than others. 

Most of the treatment systems we have seen in the journal literature appear to take advantage of 

the tendency of bacteria to adsorb to certain types of sediment particles. Treatment systems that 

reduce sediment and allow water to percolate through soil or media may be the most effective. 

We also suggest that the stormwater management manuals are not the only reference tool 

available to WSDOT for exploring treatment systems to reduce fecal coliform bacteria. 

Agricultural engineers have evaluated the bacteria removal efficiencies of various BMP systems, 

e.g. riparian buffers, lagoons, wetlands, and settling ponds. The local Natural Resource 

Conservation Service office or county conservation district may be able to help you evaluate 

your treatment systems. Ecology staff looks forward to working with WSDOT staff in 

evaluating these processes. The Technology Assessment Protocol – Ecology (TAPE) system 

should be useful in this regard. 
Stillaguamish Fecal and DO TMDL Submittal Report Page B-155 

Appendix B. 

Wastewater Treatment Plants Point Sources – 

Descriptions, NPDES Permit Limits, and Data 

Support 
Page B-156 Stillaguamish Fecal and DO TMDL Submittal Report
Stillaguamish Fecal and DO TMDL Submittal Report Page B-157 

Point Source Descriptions and NPDES Permit Limits 

Arlington Wastewater Treatment Plant 

The Arlington WWTP treatment plant discharges effluent to the Stillaguamish River just below 

the confluence of the North and South forks at RKM 28.6 (RM 17.8). The treatment processes 

include a mechanical screen and a vortex type grit chamber, biological treatment in sequencing 

batch reactors (SBRs), a flow equalization basin, and an ultraviolet (UV) disinfection system. 

Arlington WWTP effluent quality must meet secondary municipal treatment standards as 

specified in its NPDES permit (Table B1). The permit also requires monitoring of pH, fecal 

coliform bacteria, biochemical oxygen demand, total suspended solids, and discharge volume. 

Effluent monitoring of inorganic nitrogen, phosphorus, and metals is not required under the 

permit. However, Arlington does some independent monitoring to check unit processes in the 

facility (Randolph, personal communication, 2000). 

Table B1. Arlington NPDES permit limits 

Parameter Limit 

pH Shall be within the range of 6 to 9 standard units. 

Fecal Coliform 

Bacteria 

Monthly Geometric Mean = 200 organisms/100 mL 

Weekly Geometric Mean = 400 organisms/100 mL 

BOD5 

(concentration) 

Average Monthly Limit is the most stringent of the following: 

 - 30 mg/L 

 - may not exceed fifteen percent (15%) of the 

 average influent concentration 

Average Weekly Limit = 45 mg/L 

Total Suspended 

Solids 

(concentration) 

Average Monthly Limit is the most stringent of the following: 

 - 30 mg/L 

 - may not exceed fifteen percent (15%) of the 

 average effluent concentration 

Average Weekly Limit = 45 mg/L 

Parameter Design Quantity 

Monthly average flow (max. month) 2.0 MGD 

BOD5 influent loading (max. month) 4,600 lbs/day 

TSS influent loading (max. month) 3,100 lbs/day 
Page B-158 Stillaguamish Fecal and DO TMDL Submittal Report

Indian Ridge Corrections Center Wastewater Facility 

Indian Ridge Corrections Center is a small facility formerly operated by the Washington State 

Department of Social and Health Services, but now operated by Snohomish County. The facility 

discharges effluent to Jim Creek approximately 4.8 kilometers (3 miles) above the confluence 

with the South Fork Stillaguamish River. The treatment process at the facility has operated since 

1997, and it includes preliminary treatment through a mechanical fine screen, biological 

treatment in SBRs followed by ultraviolet (UV) disinfection system. The old facility was a 

package activated sludge WWTP. 

Table B2. Indian Ridge Corrections Center NPDES permit limits 

Effluent Limitationsa: Outfall # 1 

Parameter 

Average Monthly Average Weekly 

Biochemical Oxygen 

Demandb (5 day) 

30 mg/L, 6 

lbs/day 

45 mg/L, 8 lbs/day 

Total Suspended Solidsb 30 mg/L, 6 

lbs/day 

45 mg/L, 8 lbs/day 

Fecal Coliform Bacteria 100/100 mL -------- 

pH Daily minimum is equal to or greater than 6, 

and the daily maximum is less than or equal to 9. 

a

The average monthly and weekly effluent limitations are based on the arithmetic mean of the 

samples taken with the exception of fecal coliform, which is based on the geometric mean. 

b

The average monthly effluent concentration for BOD5 and Total Suspended Solids shall not exceed 

30 mg/L or 15 percent of the respective monthly average influent concentrations, whichever is more stringent.

Parameter Design Quantity 

Monthly average flow (max. month) 21,000 gpd 

BOD5 influent loading (max. month) 61 lbs/day 

Warm Beach Conference Center Wastewater Treatment Plant 

The Warm Beach Christian Camp and Conference Center is located on a bluff north of the 

unincorporated communc center accommodates groups throughout the year, but peak attendance 

is in summer. The center is planning to enlarge its facilities, so it is increasing its wastewater 

treatment capacity. 

The existing WWTP at the camp consists of biological treatment in two aerated lagoon cells 

followed by disinfection with calcium hypochlorite solution. The secondarily treated wastewater 

is discharged with subsurface drainage intercepted from around the lagoons to an unnamed 

stream tributary. NPDES permit limits are based on conventional technology for lagoon effluent 

(Table B3). 
Stillaguamish Fecal and DO TMDL Submittal Report Page B-159 

The tributary with treated effluent flows to a pond that also receives drainage water from lowlying lands to the north of the facility. Water from the pond is intermittently discharged to a 

slough leading to Port Susan via a pump and culvert through the dike. The tributary and pond 

are not on the Section 303(d) list. Part of Port Susan is on the list because of data collected from 

1989 to 1991 (Paulsen et al., 1991) near the slough at Warm Beach The slough is located 

approximately 1.2 km (0.75 miles) south of Hat Slough. 

The center is just completing construction of a managed wetland treatment system to further treat 

effluent from the lagoons. The system has specific hydraulic and biological treatment areas to 

reduce various nutrients and bacteria. The NPDES permit limits for the new plant will be more 

stringent than for the current facility. The location of the outfall from the wetland has not been 

determined as of February 2003. Potential locations include the slough currently used and a 

channel from Hat Slough. 

Table B3. Warm Beach Conference Center NPDES permit limits, interim 

Interim Effluent Limitationsa: Outfall # 1 

Parameter 

Average Monthly Average Weekly 

Biochemical Oxygen 

Demandb (5 day) (BOD5) 30 mg/L, 19 lbs/day 45 mg/L, 29 lbs/day 

Total Suspended Solids (TSS) 75 mg/L, 47 lbs/day 112 mg/L, 70 lbs/day 

Fecal Coliform Bacteria 200/100 mL 400/100 mL 

pHc Daily minimum is equal to or greater than 6, 

and the daily maximum is less than or equal to 9.

Parameter Average Monthly Maximum Daily 

Total Residual Chlorined,f --------- 2.0 mg/L 

Notes: see notes below Table B4 

Table B4. Warm Beach Conference Center NPDES permit limits, final 

Final Effluent Limitationsa: Outfall # 1 

Parameter 

Average Monthly Average Weekly 

Biochemical Oxygen 

Demandb

 (5 day) (BOD5) 30 mg/L, 19 lbs/day 45 mg/L, 29 lbs/day 

Total Suspended Solids (TSS) 75 mg/L, 47 lbs/day 112 mg/L, 70 lbs/day 

pHc Daily minimum is equal to or greater than 6, 

and the daily maximum is less than or equal to 9.

Fecal Coliform Bacteria 100/100 mL See footnote e below 

Total Residual Chlorinef 8 ug/L 19 ug/L 

Total Ammonia (NH3-N) 1.8 mg/L 3.5 mg/L 

Parameter Average Monthly Minimum Daily 

Dissolved Oxygen --------- 8.0 mg/L 

a

Interim effluent limitations were effective until April 30, 2003. Final effluent limitations became effective 

on May 1, 2003. See condition S8. “Compliance Schedule”. 

The average monthly and weekly effluent limitations are based on the arithmetic mean of the samples taken, 

with the exception of fecal coliform which is based on the geometric mean. 
Page B-160 Stillaguamish Fecal and DO TMDL Submittal Report

b

The average monthly effluent concentration for BOD5 shall not exceed 30 mg/L or 15 percent of the monthly 

average influent concentration, whichever is more stringent. 

c

Indicates the range of permitted values. When pH is continuously monitored, excursions between 5.0 and 6.0, 

or 9.0 and 10.0, shall not be considered violations provided no single excursion exceeds 60 minutes in length, and 

total excursions do not exceed 7 hours and 30 minutes per month. Any excursions below 5.0 and above 10.0 are 

violations if such values are attributable to inorganic chemical addition to the treatment process or to industrial 

contribution(s). The instantaneous maximum and minimum pH shall be reported monthly. 

d

Total residual chlorine shall be maintained which is sufficient to attain the interim fecal coliform limits specified 

above. Chlorine concentrations in excess of that necessary to reliably achieve the limits shall be avoided. e

No more than 10 percent of all samples obtained for calculating the monthly geometric mean value shall exceed 

200 colonies/100 mL. 

f

The maximum daily value for total residual chlorine is the maximum of the daily values during a calendar month. 

The daily value is defined as the arithmetic mean of the sample measurements taken during a calendar day. 

The average monthly value for total residual chlorine is the arithmetic mean of the daily values during a calendar 

month. 

Twin City Foods Wastewater Treatment Plant 

Twin City Foods, located in Stanwood, pipes its process water, repack water, and vegetable 

unloading area drainage water to an 8.5 million gallon capacity lagoon located on reclaimed 

agricultural land between the Old Stillaguamish Channel and Hat Slough. Solids in the process 

water are screened-out at the plant for animal feed. Under the most recent permit, some winter 

repack water is discharged to the Stanwood WWTP, but that will discontinue when Stanwood 

upgrades its system. Sanitary wastewater also is routed to Stanwood. 

 

The Twin City Foods lagoon water is distributed by pumps and pipes to seven spray guns for 

land application to about 600 acres. Dairy manure is also applied to about 300 acres of the same 

application areas from a separate lagoon. The lagoon effluent application rate is agronomically 

determined for nitrogen uptake to protect ground water and surface water quality. 

The area is surrounded by dikes. Many of the fields are underlain with drainage tile at a depth of 

three feet to eighteen inches that drain to the deep ditches. The deep ditch network empties to 

the Old Stillaguamish Channel and Port Susan at several tide gates. Surface monitoring sites are 

located at a few of these tide gates. 
Stillaguamish Fecal and DO TMDL Submittal Report Page B-161 

Table B5. Twin City Foods State Waste Discharge permit limits 

TMDL Determinations of Permit Limits: Fecal Coliform Data and Calculations 

Parameter Limit 

Flow 

Lagoon: 2.49 MGD Maximum 

Stanwood WWTP: 0.075 MGD Maximum (300 gpm instantaneous peak) 

 and 0.060 MGD weekly average) 

Fields: 19 inches/acre/year 

pH 

Lagoon: between 6.5 and 8.5 standard units. 

Stanwood WWTP: between 5 and 11 standard units 

Nitrogen 

Fields: 100 lbs/acre/year 

BOD5 

Stanwood WWTP: 125 lbs/day average 

150 lbs/day maximum 

The following seven tables provide a record of the fecal coliform data for receiving waters for 

each of the following wastewater treatment plants in the Stillaguamish basin: City of Arlington 

on the mainstem Stillaguamish River, Indian Ridge Corrections Facility on Jim Creek, and 

Warm Beach Conference Center south of Stanwood. 

Table B-6. Fecal Coliform Data Used to Determine Arlington WWTP Permit Limits 

 

FC Date Month log10 FC FC Date Month log10 FC FC Date Month log10 FC 

(cfu/100 

mL) yyyymmdd 1 - 12 

(cfu/100 

mL) yyyymmdd 1 - 12 

(cfu/100 

mL) yyyymmdd 1 - 12 

8 19940427 4 0.903089987 8 19940427 4 0.903089987 8 19940511 5 0.903089987 

8 19940511 5 0.903089987 49 19941212 12 1.69019608 28 19940621 6 1.447158031 

28 19940621 6 1.447158031 270 19950117 1 2.431363764 46 19940712 7 1.662757832 

46 19940712 7 1.662757832 4 19950214 2 0.602059991 139 19940815 8 2.1430148 

139 19940815 8 2.1430148 61 19950314 3 1.785329835 77 19940926 9 1.886490725 

77 19940926 9 1.886490725 10 19950417 4 1 300 19941027 10 2.477121255 

300 19941027 10 2.477121255 87 19951221 12 1.939519253 25 19941117 11 1.397940009 

25 19941117 11 1.397940009 36 19960109 1 1.556302501 120 19950508 5 2.079181246 

49 19941212 12 1.69019608 20 19960212 2 1.301029996 90 19950613 6 1.954242509 

270 19950117 1 2.431363764 19960311 3 200 19950719 7 2.301029996 

4 19950214 2 0.602059991 63 19960408 4 1.799340549 148 19950814 8 2.170261715 

61 19950314 3 1.785329835 45 19961216 12 1.653212514 73 19950912 9 1.86332286 

10 19950417 4 1 16 19970114 1 1.204119983 100 19951010 10 2 

120 19950508 5 2.079181246 116 19970212 2 2.064457989 3 19951113 11 0.477121255 

90 19950613 6 1.954242509 8 19970311 3 0.903089987 590 19960513 5 2.770852012 

200 19950719 7 2.301029996 81 19970415 4 1.908485019 83 19960611 6 1.919078092 

148 19950814 8 2.170261715 22 19971209 12 1.342422681 27 19960711 7 1.431363764 
Page B-162 Stillaguamish Fecal and DO TMDL Submittal Report

Table B-6. Fecal Coliform Data Used to Determine Arlington WWTP Permit Limits 

 

FC Date Month log10 FC FC Date Month log10 FC FC Date Month log10 FC 

(cfu/100 

mL) yyyymmdd 1 - 12 

(cfu/100 

mL) yyyymmdd 1 - 12 

(cfu/100 

mL) yyyymmdd 1 - 12 

73 19950912 9 1.86332286 11 19980101 1 1.041392685 91 19960814 8 1.959041392 

100 19951010 10 2 9 19980318 3 0.954242509 100 19960917 9 2 

3 19951113 11 0.477121255 15 19980426 4 1.176091259 3200 19961015 10 3.505149978 

87 19951221 12 1.939519253 31 19981202 12 1.491361694 181 19961113 11 2.257678575 

36 19960109 1 1.556302501 19990114 1 58 19970513 5 1.763427994 

20 19960212 2 1.301029996 21 19990203 2 1.322219295 93 19970610 6 1.968482949 

 19960311 3 6 19990301 3 0.77815125 101 19970715 7 2.004321374 

63 19960408 4 1.799340549 4 19990415 4 0.602059991 27 19971014 10 1.431363764 

590 19960513 5 2.770852012 36 19991202 12 1.556302501 12 19971112 11 1.079181246 

83 19960611 6 1.919078092 9 20000105 1 0.954242509 48 19980513 5 1.681241237 

27 19960711 7 1.431363764 20000207 2 9 19980617 6 0.954242509 

91 19960814 8 1.959041392 4 20000315 3 0.602059991 52 19980720 7 1.716003344 

100 19960917 9 2 140 20000406 4 2.146128036 41 19980813 8 1.612783857 

3200 19961015 10 3.505149978 3 20001213 12 0.477121255 70 19980923 9 1.84509804 

181 19961113 11 2.257678575 8 20010110 1 0.903089987 26 19981007 10 1.414973348 

45 19961216 12 1.653212514 20010207 2 17 19981102 11 1.230448921 

16 19970114 1 1.204119983 22 20010314 3 1.342422681 28 19990506 5 1.447158031 

116 19970212 2 2.064457989 42 20010411 4 1.62324929 96 19990609 6 1.982271233 

8 19970311 3 0.903089987 63 20011206 12 1.799340549 14 19990712 7 1.146128036 

81 19970415 4 1.908485019 20020109 1 30 19990802 8 1.477121255 

58 19970513 5 1.763427994 90 20020212 2 1.954242509 30 19990913 9 1.477121255 

93 19970610 6 1.968482949 11 20020313 3 1.041392685 40 19991013 10 1.602059991 

101 19970715 7 2.004321374 14 19991104 11 1.146128036 

27 19971014 10 1.431363764 Geomean 1.348503847 4 20000504 5 0.602059991 

12 19971112 11 1.079181246 0.503510328 9 20000608 6 0.954242509 

22 19971209 12 1.342422681 

90th 

%tile 1.993802684 72 20000713 7 1.857332496 

11 19980101 1 1.041392685 

# of 

samples 34 63 20000808 8 1.799340549 

9 19980318 3 0.954242509 19 20000912 9 1.278753601 

15 19980426 4 1.176091259 16 20001004 10 1.204119983 

48 19980513 5 1.681241237 84 20001108 11 1.924279286 

9 19980617 6 0.954242509 280 20010509 5 2.447158031 

52 19980720 7 1.716003344 24 20010604 6 1.380211242 

41 19980813 8 1.612783857 120 20010705 7 2.079181246 

70 19980923 9 1.84509804 610 20010806 8 2.785329835 

26 19981007 10 1.414973348 27 20010905 9 1.431363764 

17 19981102 11 1.230448921 34 20011003 10 1.531478917 

31 19981202 12 1.491361694 24 20011105 11 1.380211242 

 19990114 1 

21 19990203 2 1.322219295 Geomean 1.708157688 51 May to 

6 19990301 3 0.77815125 0.546928708 November 

4 19990415 4 0.602059991 

90th 

%tile 2.40910152 257 

28 19990506 5 1.447158031 

# of 

samples 54 

96 19990609 6 1.982271233 

14 19990712 7 1.146128036 
Stillaguamish Fecal and DO TMDL Submittal Report Page B-163 

Table B-6. Fecal Coliform Data Used to Determine Arlington WWTP Permit Limits 

 

FC Date Month log10 FC FC Date Month log10 FC FC Date Month log10 FC 

(cfu/100 

mL) yyyymmdd 1 - 12 

(cfu/100 

mL) yyyymmdd 1 - 12 

(cfu/100 

mL) yyyymmdd 1 - 12 

30 19990802 8 1.477121255 

30 19990913 9 1.477121255 

40 19991013 10 1.602059991 

14 19991104 11 1.146128036 

36 19991202 12 1.556302501 

9 20000105 1 0.954242509 

 20000207 2 

4 20000315 3 0.602059991 

140 20000406 4 2.146128036 

4 20000504 5 0.602059991 

9 20000608 6 0.954242509 

72 20000713 7 1.857332496 

63 20000808 8 1.799340549 

19 20000912 9 1.278753601 

16 20001004 10 1.204119983 

84 20001108 11 1.924279286 

3 20001213 12 0.477121255 

8 20010110 1 0.903089987 

 20010207 2 

22 20010314 3 1.342422681 

42 20010411 4 1.62324929 

280 20010509 5 2.447158031 

24 20010604 6 1.380211242 

120 20010705 7 2.079181246 

610 20010806 8 2.785329835 

27 20010905 9 1.431363764 

34 20011003 10 1.531478917 

24 20011105 11 1.380211242 

63 20011206 12 1.799340549 

 20020109 1 

90 20020212 2 1.954242509 

11 20020313 3 1.041392685 

 

 Geomean 1.569200522 1.559693083 36 June 2000 - March 2002 TMDL study period 

 0.556248941 0.544265941 

 

90th 

%tile 2.282089165 2.257224312 181 

 

# of 

samples 88 20 
Page B-164 Stillaguamish Fecal and DO TMDL Submittal Report

Table B-7. Fecal Coliform Data Used for Permit Limit Calculations for Indian Ridge Corrections Facility 

 

Jim Creek at Whites Rd (above WWTP): Collected by the Stillaguamish Tribe and Natural Resources Department 

 

FC Date Month log10 FC 

(cfu/100 mL) yyyymmdd 1 - 12 

36 5/19/1998 5 1.5563025 

270 7/28/1998 7 2.4313638 

35 9/15/1998 9 1.544068 

13 1/19/1999 1 1.1139434 

5 3/9/1999 3 0.69897 

14 5/11/1999 5 1.146128 

28 7/20/1999 7 1.447158 

59 9/21/1999 9 1.770852 

20 11/16/1999 11 1.30103 

17 1/12/2000 1 1.2304489 

30 3/22/2000 3 1.4771213 FC Date Month log10 FC 

4 5/24/2000 5 0.60206 

(cfu/100 

mL) yyyymmdd 1 - 12 

55 7/11/2000 7 1.7403627 55 7/11/2000 7 1.7403627 

16 11/15/2000 11 1.20412 16 11/15/2000 11 1.20412 

4 3/15/2001 3 0.60206 4 3/15/2001 3 0.60206 

24 11/15/2001 11 1.3802112 24 11/15/2001 11 1.3802112 

14 3/15/2002 3 1.146128 14 3/15/2002 3 1.146128 

23 6/15/2002 6 1.3617278 23 6/15/2002 6 1.3617278 

 

 Geomean 1.3196698 21 

All 

data Geomean 1.2391016 17 2000 to 

Critical 

Condition ---

> 0.441165 0.3746736 2002 data 

 

90th 

%tile 1.8850668 77 

90th 

%tile 1.7192833 52 

 

# of 

samples 18 

# of 

samples 6 

 

Jim Creek at Mouth: Collected by Stillaguamish Tribe Natural Resources and Ecology 

 

FC Date Month log10 FC 

(cfu/100 mL) yyyymmdd 1 - 12 

22 4/22/1996 4 1.3424227 

70 5/15/1996 5 1.845098 

29 6/19/1996 6 1.462398 

182 8/14/1996 8 2.2600714 

710 9/18/1996 9 2.8512583 

160 11/6/1996 11 2.20412 

7 1/15/1997 1 0.845098 

100 3/26/1997 3 2 

55 5/21/1997 5 1.7403627 

200 7/15/1997 7 2.30103 

620 9/17/1997 9 2.7923917 
Stillaguamish Fecal and DO TMDL Submittal Report Page B-165 

Table B-7. Fecal Coliform Data Used for Permit Limit Calculations for Indian Ridge Corrections Facility 

 

Jim Creek at Whites Rd (above WWTP): Collected by the Stillaguamish Tribe and Natural Resources Department 

 

FC Date Month log10 FC 

(cfu/100 mL) yyyymmdd 1 - 12 

22 5/19/1998 5 1.3424227 

220 7/28/1998 7 2.3424227 

38 9/15/1998 9 1.5797836 

11 1/19/1999 1 1.0413927 

20 5/11/1999 5 1.30103 

41 7/20/1999 7 1.6127839 

28 9/21/1999 9 1.447158 

21 11/16/1999 11 1.3222193 

22 11/15/2000 11 1.3424227 

20 3/15/2001 3 1.30103 

320 6/12/2001 6 2.50515 

150 6/13/2001 6 2.1760913 

160 11/14/2001 11 2.20412 

140 11/15/2001 11 2.146128 

20 11/15/2001 11 1.30103 

55 3/15/2002 3 1.7403627 

55 6/15/2002 6 1.7403627 

 

 Geomean 1.7889343 62 

April 1996 - 

June 2002 1.82852192 67 June 2000 - June 2002 

 0.5233068 0.45123574 

 

90th 

%tile 2.4596043 288 2.40682565 255 

 

# of 

samples 28 9 

 

 Using WQ Hydro: geomean = 55 

 90th percentile = 320 

 

Table 26 values based on these more sophisticated statistical 

analyses 

 

Jim Creek at Whites Rd (above WWTP): Collected by the Stillaguamish Tribe 

 

(cfu/100 mL) yyyymmdd 1 - 12 

(cfu/100 

mL) yyyymmdd 1 - 12 

70 5/15/1996 5 1.845098 22 4/22/1996 4 1.3424227 

29 6/19/1996 6 1.462398 7 1/15/1997 1 0.845098 

182 8/14/1996 8 2.2600714 100 3/26/1997 3 2 

710 9/18/1996 9 2.8512583 11 1/19/1999 1 1.0413927 

160 11/6/1996 11 2.20412 20 3/15/2001 3 1.30103 

55 5/21/1997 5 1.7403627 55 3/15/2002 3 1.7403627 

200 7/15/1997 7 2.30103 

620 9/17/1997 9 2.7923917 Geomean 1.3783843 24 

 

December 

22 5/19/1998 5 1.3424227 0.429574 to April 

220 7/28/1998 7 2.3424227 

90th 

%tile 1.9289263 85 
Page B-166 Stillaguamish Fecal and DO TMDL Submittal Report

Table B-7. Fecal Coliform Data Used for Permit Limit Calculations for Indian Ridge Corrections Facility 

 

Jim Creek at Whites Rd (above WWTP): Collected by the Stillaguamish Tribe and Natural Resources Department 

 

FC Date Month log10 FC 

(cfu/100 mL) yyyymmdd 1 - 12 

38 9/15/1998 9 1.5797836 

# of 

samples 6 

20 5/11/1999 5 1.30103 

41 7/20/1999 7 1.6127839 

28 9/21/1999 9 1.447158 

21 11/16/1999 11 1.3222193 

22 11/15/2000 11 1.3424227 

320 6/12/2001 6 2.50515 

150 6/13/2001 6 2.1760913 

160 11/14/2001 11 2.20412 

140 11/15/2001 11 2.146128 

20 11/15/2001 11 1.30103 

55 6/15/2002 6 1.7403627 

 

 Geomean 1.9009025 80 May - November 

 0.5089646 

 

90th 

%tile 2.5531916 357 

 

# of 

samples 22 

 

b-Table B-8. Fecal Coliform Data Used to Determine Warm Beach WWTP Permit Limits 

 

Warm Beach Conference Center WWTP -- Option (1) Discharge at 

Warm Beach 

 

FC Date Month log10 FC 

(cfu/100 

mL) yyyymmdd 1 - 12 

4.5 20010227 2 0.65321251 

17 20010329 3 1.23044892 

2 20010419 4 0.30103 

13 20010509 5 1.11394335 

20 20020102 1 1.30103 

26 20020206 2 1.41497335 

20 20020306 3 1.30103 

130 20020403 4 2.11394335 

70 20020501 5 1.84509804 

 

 Geomean 1.84765471 70 All data 

 0.71326495 

 90th %tile 2.76177507 578 
Stillaguamish Fecal and DO TMDL Submittal Report Page B-167 

b-Table B-8. Fecal Coliform Data Used to Determine Warm Beach WWTP Permit Limits 

 

Warm Beach Conference Center WWTP -- Option (1) Discharge at 

Warm Beach 

 

# of 

samples 19 

 

 FC Date Month log10 FC FC Date Month log10 FC 

 

(cfu/100 

mL) yyyymmdd 1 - 12 

(cfu/100 

mL) yyyymmdd 1 - 12 

 240 20010606 6 2.38021124 4.5 20010227 2 0.6532125 

 79 20010711 7 1.89762709 17 20010329 3 1.2304489 

 350 20010822 8 2.54406804 2 20010419 4 0.30103 

 170 20010919 9 2.23044892 13 20010509 5 1.1139434 

 140 20011017 10 2.14612804 20 20020102 1 1.30103 

 130 20011119 11 2.11394335 26 20020206 2 1.4149733 

 310 20020605 6 2.49136169 20 20020306 3 1.30103 

 500 20020703 7 2.69897 130 20020403 4 2.1139434 

 560 20020807 8 2.74818803 70 20020501 5 1.845098 

 380 20020904 9 2.5797836 Dec-May 

 Geomean 1.2527455 18 

 Geomean 2.383073 242 

JuneNov 0.5486904 

Critical 

Condition 

-----------> 0.27828333 

90th 

%tile 1.9559471 90 

 90th %tile 2.73972092 549 

# of 

samples 9 

 

# of 

samples 10 

 

 Using WQ Hydro: geomean = 253 

 90th percentile = 543 

 Table 26 values based on these more sophisticated statistical analyses 

 

Table B-9. Fecal Coliform Data Used to Determine WWTP Permit Limits 

 

Warm Beach Conference Center WWTP - Option (2) Discharge at Hat Slough 

 

 Hat Slough West Branch South Branch South Branch 

 120* 121* 122* 122* 

Date 

7/27/1998 50 30 50 *120, 121 and 122 refer to 1.69897 

8-27-98 33 77 62 Port Susan water quality 1.7923917 

9-09-98 80 50 30 sample sites 1.4771213 

9-23-98 80 50 23 1.3617278 

10-07-98 80 80 130 2.1139434 

10-21-98 50 50 110 2.0413927 

11-10-98 50 50 
Page B-168 Stillaguamish Fecal and DO TMDL Submittal Report

Table B-9. Fecal Coliform Data Used to Determine WWTP Permit Limits 

 

Warm Beach Conference Center WWTP - Option (2) Discharge at Hat Slough 

 

 Hat Slough West Branch South Branch South Branch 

 120* 121* 122* 122* 

11-18-98 13 26 8 0.90309 

12-03-98 80 80 50 1.69897 

12-15-98 17 17 2 0.30103 

1-13-99 2 4 8 0.90309 

2-03-99 2 23 21 1.3222193 

2-18-99 2 13 4 0.60206 

2-23-99 22 13 50 1.69897 

3-18-99 8 8 8 0.90309 

3-31-99 22 7 17 1.2304489 

4-15-99 2 8 4 0.60206 

4-21-99 23 50 80 1.90309 

5-05-99 13 17 2 0.30103 

5-20-99 30 22 22 1.3424227 

6-07-99 2 11 1.5 0.1760913 

6-15-99 110 70 30 1.4771213 

7-01-99 50 70 17 1.2304489 

7-15-99 1.5 2 2 0.30103 

7-29-99 17 21 30 1.4771213 

8-03-99 13 14 30 1.4771213 

8-31-99 13 11 80 1.90309 

9/14/1999 2 11 50 1.69897 9/28/1999 80 23 80 1.90309 10/13/1999 50 70 130 2.1139434 11/10/1999 70 30 30 1.4771213 

12/9/1999 11 11 8 0.90309 1/26/2000 13 30 50 1.69897 2/9/2000 13 4 17 1.2304489 2/23/2000 17 50 50 1.69897 4/11/2000 11 2 4 0.60206 

4/26/2000 17 23 1.5 0.1760913 5/9/2000 14 8 4 0.60206 5/23/2000 1.5 50 1.69897 

6/7/2000 23 50 17 1.2304489 

6/21/2000 13 4 13 1.1139434 

7/6/2000 11 13 8 0.90309 

7/20/2000 30 23 8 0.90309 8/3/2000 23 30 50 1.69897 8/31/2000 30 23 80 1.90309 9/14/2000 70 80 130 2.1139434 9/28/2000 13 23 23 1.3617278 

10/18/2000 45 78 20 1.30103 

11/2/2000 13 30 36 1.5563025 11/15/2000 4 50 23 1.3617278 
Stillaguamish Fecal and DO TMDL Submittal Report Page B-169 

Table B-9. Fecal Coliform Data Used to Determine WWTP Permit Limits 

 

Warm Beach Conference Center WWTP - Option (2) Discharge at Hat Slough 

 

 Hat Slough West Branch South Branch South Branch 

 120* 121* 122* 122* 

11/29/2000 23 30 11 1.0413927 12/5/2000 2 1/25/2001 4 

2/15/2001 11 17 23 1.3617278 

2/27/2001 70 50 1.69897 3/14/2001 50 14 1.146128 3/29/2001 7 30 4 0.60206 4/19/2001 17 

4/26/2001 23 8 0.90309 5/9/2001 7.8 1.5 2 0.30103 

5/24/2001 23 30 1.4771213 6/6/2001 23 11 13 1.1139434 

6/21/2001 23 23 1.3617278 7/11/2001 22 50 110 2.0413927 

7/31/2001 11 50 50 1.69897 

8/9/2001 50 30 50 1.69897 8/22/2001 240 240 130 2.1139434 9/5/2001 30 30 240 2.3802112 

10/4/2001 23 130 50 1.69897 

10/18/2001 17 50 50 1.69897 

11/8/2001 8 

11/19/2001 13 13 14 1.146128 

12/5/2001 13 4 0.60206 

1/17/2002 11 

2/8/2002 13 

2/28/2002 4 Geomean 1.3173102 21

3/5/2002 2 4 0.5420266 

3/21/2002 22 22 90th %tile 2.0119715 103

4/18/2002 2 50 # of samples 68 

5/16/2002 13 13 

5/29/2002 50 

6/13/2002 30 70 

6/27/2002 

6/7/2000 23 50 17 1.2304489 

6/21/2000 13 4 13 1.1139434 

7/6/2000 11 13 8 0.90309 7/20/2000 30 23 8 0.90309 8/3/2000 23 30 50 1.69897 8/31/2000 30 23 80 1.90309 9/14/2000 70 80 130 2.1139434 

9/28/2000 13 23 23 1.3617278 

10/18/2000 45 78 20 1.30103 11/2/2000 13 30 36 1.5563025 
Page B-170 Stillaguamish Fecal and DO TMDL Submittal Report

Table B-9. Fecal Coliform Data Used to Determine WWTP Permit Limits 

 

Warm Beach Conference Center WWTP - Option (2) Discharge at Hat Slough 

 

 Hat Slough West Branch South Branch South Branch 

 120* 121* 122* 122* 

11/15/2000 4 50 23 1.3617278 11/29/2000 23 30 11 1.0413927 12/5/2000 2 

1/25/2001 4 

2/15/2001 11 17 23 1.3617278 2/27/2001 70 50 1.69897 3/14/2001 50 14 1.146128 3/29/2001 7 30 4 0.60206 

4/19/2001 17 4/26/2001 23 8 0.90309 

5/9/2001 7.8 1.5 2 0.30103 5/24/2001 23 30 1.4771213 

6/6/2001 23 11 13 1.1139434 6/21/2001 23 23 1.3617278 

7/11/2001 22 50 110 2.0413927 

7/31/2001 11 50 50 1.69897 8/9/2001 50 30 50 1.69897 8/22/2001 240 240 130 2.1139434 

9/5/2001 30 30 240 2.3802112 10/4/2001 23 130 50 1.69897 

10/18/2001 17 50 50 1.69897 

11/8/2001 8 

11/19/2001 13 13 14 1.146128 

12/5/2001 13 4 0.60206 

1/17/2002 11 

2/8/2002 13 

2/28/2002 4 

3/5/2002 2 4 

3/21/2002 22 22 

4/18/2002 2 50 

5/16/2002 13 13 

5/29/2002 50 

6/13/2002 30 70 

6/27/2002 Last 30 samples 

 Geomean 1.3844723 24

 Critical Condition -----------> 0.4874862 

 90th %tile 2.0092347 102

 # of samples 30 

 
Stillaguamish Fecal and DO TMDL Submittal Report Page C-171 

Appendix C. 

Monitoring Locations for Ecology July 2004 

Technical Study 
Page C-172 Stillaguamish Fecal and DO TMDL Submittal Report
Stillaguamish Fecal and DO TMDL Submittal Report Page C-173 

Locations 

Locations of monitoring sites are provided in Table C-1 and shown in Figures C-1 through C-3. 

Additional information about the Ecology TMDL water quality monitoring between August 

2000 and November 2001 is provided in Data Summary: Stillaguamish River Watershed Fecal 

Coliform, Dissolved Oxygen, pH, Mercury, and Arsenic Total Maximum Daily Load Study, on 

Ecology’s website at: http://www/ecy.wa.gov/biblio/0403037.html.

Table C-1. Listing of monitoring stations

Station ID Station Name Latitude Longitude 

River 

Mile 

River 

Kilometer Survey/s 

05TARLIN2 Arlington WWTP effluent 48.2031 122.1279 - - C, D, E, H 

05TARMST Armstrong Creek at the hatchery gauging station 48.2184 122.1362 1.0 1.6 E, H 

05TCHUPK Church Creek at the park off Lindstrom Road 48.2413 122.3257 2.1 3.4 B 

05TCHURH Church Creek/Jorgenson Slough at Marine Drive 48.2312 122.3466 0.5 0.8 A, F, G, H 

05TCONFL1 Confluence of North and South Forks of the Stilliguamish River at Hwy. 9 48.2037 122.1286 17.8 28.6 C, D, E, I 

05TCOOK Cook Slough at Hwy. 530 bridge near Silvana 48.1966 122.2438 7.8 12.6 C, D, E, H 

05TDOUG4 Douglas Slough south of Hwy. 532 48.2399 122.3759 0.1 0.2 A, F, H 

05TGLAD Glade Bekken at Silvana Terrace Road 48.2045 122.2902 0.5 0.8 C, D, E, H 

05THARAR Mouth of Harvey Armstrong Creek 48.2105 122.1511 0.1 0.2 C, D, E 

05TIRVIN Irvine Slough at dike pump station 48.2406 122.3689 0.1 0.2 A, F, H 

05TJIMCK Jim Creek at Jordan Road 48.1988 122.0938 0.1 0.2 H 

05TJUNIP Juniper Beach off Juniper Beach Road on Camano Island 48.2279 122.4082 - - J 

05TKACK Kackman Creek at 252nd Street NE 48.2246 122.1616 0.9 1.4 E, H 

05TMAR1 March Creek at Mouth 48.1929 122.1639 0.1 0.2 C, D, E 

05TMARIN2 Mainstem Stillaguamish River at Hat Slough off Marine Drive 48.2109 122.3378 1.9 3.1 

C, D, E, G, 

H, I 

05TMARIN2 Mainstem Stillaguamish River at Hat Slough boat launch 48.2114 122.3391 1.7 2.7 B 

05TMARSH Mouth of March Creek at 220th Street NE 48.1927 122.1655 0.9 1.4 H 

05TMARTH Martha Lake Creek at Soundview Drive 48.1743 122.3609 0.1 0.2 I 

05TMARTOL Martha Lake Creek outlet to Warm Beach 48.1754 122.3622 0.0 0.0 I 

05TMILLR4 Miller Creek at Miller Road 48.2216 122.3179 0.2 0.2 A, F, H 

05TMIXZO Mainstem Stillaguamish River below Arlington WWTP outfall 48.2030 122.1316 17.6 28.3 C, D, I 

05TMS3 Mainstem Stillaguamish River at Old Channel diversion 48.2087 122.3225 2.8 4.4 C, D, E 

05TMS6 Mainstem Stillaguamish River below Silvana 48.2034 122.2765 5.7 9.2 C, D, E 

05TMS111, 2 Mainstem Stillaguamish River at Interstate 5 bridge 48.1970 122.2107 11.2 17.9 

C, D, E, G, 

H 

05TMS12 Mainstem Stillaguamish River at WDFWS access 48.1991 122.1931 12.1 19.5 I 

05TMS131 Mainstem Stillaguamish River below March Creek 48.1916 122.1823 12.9 20.8 C, D, E 

05TMS151 Mainstem Stillaguamish River below Armstrong Creek 48.2072 122.1544 14.9 24.0 C, D, E 

05TMS17 Mainstem Stillaguamish River at Dike Road 48.1999 122.1481 17.0 27.4 C, D, E, H 

05TNFCIC2, 3 North Fork Stillaguamish River at Cicero bridge 48.2679 122.0135 9.5 15.3 E, G, H 

05TNFCPO2 North Fork Stillaguamish River at C-Post Bridge 48.2829 121.8304 21.0 33.8 E, H 

05TNFTWI2 Mouth of the North Fork Stillaguamish River at Twin Rivers Park 48.2038 122.1274 0.1 0.2 

B, C, D, E, 

H 

05TNFWHI2 North Fork Stillaguamish River at Whitman Road bridge 48.2722 121.8879 17.6 28.3 B, E, H 

05TNORTH North branch of the mainstem Stillaguamish River at Hwy. 530 bridge 48.2103 122.2470 7.5 12.1 C, D, E, H 

05TOC1 Old Stillaguamish River Channel near Irvine Slough 48.2394 122.3684 1.4 2.3 A, F, H 

05TOC2 Old Stillaguamish River Channel above the Stanwood WWTP outfall 48.2361 122.3564 3.4 5.5 A, F, H 

05TOC3 Old Stillaguamish River Channel at the Marine Drive bridge 48.2257 122.3382 5.1 8.2 A, F, G, H 

05TOC4 Old Stillaguamish River Channel at the Norman Road bridge 48.2132 122.3268 7.4 11.9 A, F, H 

05TPILCH2 Pilchuck Creek at Jackson Gulch Road 48.2101 122.2255 0.1 0.2 C, D, E, H 
Page C-174 Stillaguamish Fecal and DO TMDL Submittal Report

Station ID Station Name Latitude Longitude 

River 

Mile 

River 

Kilometer Survey/s 

05TPILDOWN 

Downstream of the mouth of Pilchuck Creek in North Stillaguamish 

Slough 48.2049 122.2281 9.3 15.0 D 

0TPILUP Upstream of the mouth of Pilchuck Creek in North Stillaguamish Slough 48.2085 122.2195 9.5 15.3 D 

05TPORT2 Portage Creek at the 212th Street bridge 48.1885 122.2335 1.1 1.8 C, D, E, H 

05TSFGRA2 South Fork Stillaguamish below Granite Falls 48.0959 121.9739 33.5 53.9 E, H 

05TSFJOR2 South Fork Stillaguamish at Jordan walkway bridge 48.1475 122.0386 26.1 42.0 B, E, H 

05TSFTWI2 Mouth of the South Fork Stillaguamish River at Twin Rivers Park 48.2036 122.1273 0.1 0.2 

B, C, D, E, 

G, H 

05TSILVA Mainstem Stillaguamish River below Silvana off Norman Road 48.2083 122.2835 4.6 7.4 H 

05TSOUTH South Pass at the end of Eide Road 48.2261 122.3857 0.5 0.8 A, F, H, I 

05TSTAN4 Stanwood WWTP effluent 48.2362 122.3577 - - A, F, H 

05TTCF1 Twin City Foods Drain # 1 at dike 48.2382 122.3761 0.1 0.2 A, F, H, I 

05TTCF2 Twin City Foods Drain # 2 on Thomle Road 48.2261 122.3670 0.1 0.2 A, F, H 

05TTCF34 Twin City Foods Drain # 3 on Thomle Road 48.2264 122.3627 0.1 0.2 A, F, H 

05TTCF4 Twin City Foods Drain #4 to Hat Slough 48.1983 122.3626 0.1 0.2 C, D, I 

05TTCF5 Twin City Foods Drain # 5 at footbridge above Thomle Road 48.2289 122.3524 0.2 0.3 A, F, H 

05TUNIDE Unnamed Creek #0456 at the end of Soundview Drive 48.1647 122.3691 0.1 0.2 I 

05TWAREF Warm Beach WWTP effluent at Warm Beach 48.1885 122.3501 - - I 

05TWARSL Pump pond slough at Warm Beach 48.1886 122.3527 0.0 0.0 I 

05TWARTG Field ditch to pump pond at Warm Beach 48.1889 122.3520 0.1 0.2 I 

05TWARUP Warm Beach Creek upstream of WWTP outfall 48.1887 122.3496 0.2 0.3 I 

05TWARUS Warm Beach Creek above camp stables 48.1901 122.3446 0.5 0.8 I 

05TWEST 

West pass of Old Stillaguamish River Channel at Hwy. 532 bridge in 

Stanwood 48.2399 122.3854 1.0 1.6 A, F, H 1

Continously 

recording probe 

deployed at these 

sites for Survey C. 

2

E. coli sampled at these sites in addition to fecal coliform and enterococcus. 

3

Samples taken at 05TNFTWI on 6/12/2001 and 10/3/2001. 

4

Sampled during June 2001 storm event only. 
Stillaguamish Fecal and DO TMDL Submittal Report 

Figure C-1. Sites in the lower river basin including the Old Channel and mainstem monitored in 2000 and 2001 for fbacteria, dissolved oxygen and other conventional parameters (Ecology TMDL Data Summary August 2004). 
Page C-176 Stillaguamish Fecal and DO TM

Figure C-2. Sites along mainstem of Stillaguamish River monitored for fecal coliform bacteria, dissolved conventional parameters (Ecology August 2004). 
Stillaguamish Fecal and DO TMDL Submittal Report 

Figure C-3. Sites along the North and South Forks of the Stillaguamish River monitored for fecal coliform bacteria, oxygen, pH, and other conventional parameters (Ecology August 2004). 
Page C-178 Stillaguamish Fecal and DO TM
Stillaguamish Fecal and DO TMDL Submittal Report Page D-179 

Appendix D. 

Equations and Examples of Calculations 
Page D-180 Stillaguamish Fecal and DO TMDL Submittal Report
Stillaguamish Fecal and DO TMDL Submittal Report Page D-181 

Statistical Theory of Rollback 

The statistical rollback method proposed by Ott (1995) describes a way to use a numeric 

distribution of a water quality parameter to estimate the distribution after abatement processes 

are applied to sources. The method relies on basic dispersion and dilution assumptions and their 

effect on the distribution of a chemical or a bacterial population at a monitoring site downstream 

from a source. It then provides a statistical estimate of the new population after a chosen 

reduction factor is applied to the existing pollutant source. In the case of the TMDL, compliance 

with the most restrictive of the dual fecal coliform criteria will determine the reduction factor 

needed. 

As with many water quality parameters, fecal coliform (FC) counts collected over time at an 

individual site usually follows a lognormal distribution. That is, over the course of a year’s 

sampling period most of the counts are low, but a few are much higher. When monthly FC data 

are plotted on a logarithmic-probability graph (the open diamonds in Figure D-1), they appear to 

form nearly a straight line. 

The 50th percentile, an estimate of the geometric mean, and the 90th percentile, a representation 

of the level over which 10 percent of the samples lie, can be located along a line plotted from an 

equation estimating the original monthly FC data distribution. In the graphical example, these 

numbers are 75 cfu/100 mL and 383 cfu/100 mL, respectively. Using the statistical rollback 

method, the 90th percentile value is then reduced to 200 cfu/100 mL (Class A 90th percentile 

criterion), since 75 cfu/100 mL meets the Class A geometric mean criterion. The new 

distribution is plotted parallel to the original. The estimate of the geometric mean for this new 

distribution, located at the 50th percentile, is 39 cfu/100 mL. The result is a geometric mean 

target of a sample distribution that would likely have less than 10 percent of its samples over 200 

cfu/100 mL. A 48 percent FC reduction is required from combined sources to meet this target 

distribution from the simple calculation: (383 - 200) / 383 = 0.477 * 100 = 48%. 

The following is a brief summary of the major theorems and corollaries for the statistical theory 

of rollback (STR) from Environmental Statistics and Data Analysis by Ott (1995). 

1. If Q = the concentration of a contaminant at a source, and D = the dilution-diffusion factor, 

and X = the concentration of the contaminant at the monitoring site, then X = Q*D. 

2. Successive random dilution and diffusion of a contaminant Q in the environment often result 

in a lognormal distribution of the contaminant X at a distant monitoring site. 

3. The coefficient of variation (CV) of Q is the same before and after applying a “rollback”; 

i.e., the CV in the post-control state will be the same as the CV in the pre-control state. The 

rollback factor = r, a reduction factor expressed as a decimal (a 70% reduction would be a 

rollback factor of 0.3). The random variable Q represents a pre-control source output state 

and rQ represents the post-control state. 

4. If D remains consistent in the pre-control and post-control states (long-term hydrological and 

climatic conditions remain unchanged), then CV(Q)*CV(D)=CV(X), and CV(X) will be the 

same before and after the rollback is applied. 
Page D-182 Stillaguamish Fecal and DO TMDL Submittal Report

5. If X is multiplied by the rollback factor r, then the variance in the post-control state will be 

multiplied by r2

, and the post-control standard deviation will be multiplied by r. 

6. If X is multiplied by the rollback factor r, the quantiles of the concentration distribution will 

be scaled geometrically. 

7. If any random variable is multiplied by a factor r, then its expected value and standard 

deviation also will be multiplied by r, and its CV will be unchanged. (Ott uses “expected 

value” for the mean.) 

383 cfu/100 mL 

90th-percentile

Estimate of the 

Geometric Mean 

200 cfu/100 mL 

Original FC Distribution 

Target Geometric Mean

Target 90th-percentile

39 cfu/100 mL 

Required Reduction

75 cfu/100 mL 

Figure D-1. Graphical demonstration of the statistical rollback method (Ott, 1995) used to 

calculate the fecal coliform TMDL target on the 

lower Nooksack River. 
Stillaguamish Fecal and DO TMDL Submittal Report Page D-183 

Statistical Formula for Deriving Percentile Values 

The 90th percentile value for a population can be derived in a couple of ways. The set of FC 

counts collected at a site were subjected to a statistically-based formula used by the federal Food 

and Drug Administration to evaluate growing areas for shellfish sanitation. The National 

Shellfish Sanitation Program Model Ordinance (USFDA, 2000) states: 

The estimated 90th percentile shall be calculated by: 

(a) Calculating the arithmetic mean and standard deviation of the sample result logarithms 

(base 10). 

(b) Multiplying the standard deviation in (a) by 1.28. 

(c) Adding the product from (b) to the arithmetic mean. 

(d) Taking the antilog (base 10) of the results in (c) to get the estimated 90th percentile. 

(e) The most probable number (MPN) values that signify the upper or lower range of 

sensitivity of the MPN tests in the 90th percentile calculation shall be increased or decreased 

by one significant number. 

The 90th percentile derived using this formula assumes a lognormal distribution of the FC data. 

The variability in the data is expressed by the standard deviation, and with some data sets it is 

possible to calculate a 90th percentile greater than any of the measured data. 

 

The 10th and 90th percentile values for pH and dissolved oxygen were calculated using the 

EXCEL® spreadsheet based on the rank order of the data set. The 10th percentile of a data set 

containing n data is estimated as at the k

th ordered datum: 

 

 k = ((n - 1)*0.1) + 1 

Likewise, the 90th percentile is calculated: 

 

 k = ((n - 1)*0.9) + 1 

For example, given a simple data set of 10 datum in the following rank order: 

 6.94, 7.05, 7.07, 7.09, 7.3, 7.32, 7.42, 7.45, 7.52, 7.63 

 

the 10th percentile is located at ((10 – 1)*0.1) + 1 = 1.9. Between rank 1 (6.94) and rank 2 (7.05), 

the 10th percentile is estimated as 7.04. The 90th percentile is located at ((10 – 1)*0.9) + 1 = 9.1. 

Between rank 9 (7.52) and rank 10 (7.63), the 90th percentile is estimated as 7.53. 

Beales Ratio Equation 

Beales ratio estimator from Principles of Surface Water Quality Modeling and Control by 

Thomann and Mueller (1987) provides a mass loading rate estimate of a pollutant. The formula 
Page D-184 Stillaguamish Fecal and DO TMDL Submittal Report

for the unbiased stratified ratio estimator is used when continuous flow data are available for 

sites with less frequent pollutant sample data. The average load is then: 

( ) ( ) ( )

( ) ( ) ⎥

⎥

⎥

⎦

⎤

⎢

⎢

⎢

⎣

⎡

+ ⋅

+ ⋅ = ⋅ ⋅ 2 1 2 1

1 1

Q c

c QW c

c

c

p p

S Q n

S Q W

n

Q

W W Q

where, 

W p is the estimated average load for the period, 

p is the period, 

Q p is the mean flow for the period, 

W c is the mean daily loading for the days on which pollutant samples were collected, 

Qc is the mean daily flow for days when samples were collected, 

n is the number of days when pollutant samples were collected. 

The Simple Method to Calculate Urban Stormwater Loads 

L = Annual load in lbs 

R = Annual runoff in inches 

C = Pollutant concentration in mg/L 

A = Area in acres 

0.226 = unit conversion factor 

L = 0.226 * R * C * A 

L = Annual load in billions of colonies 

C = Bacteria concentration in #/100 mL 

1.03 E-3 = unit conversion factor 

L = 1.03 E-3 * R * C * A 

R = P * Pj * Rv 

P = Annual rainfall in inches 

Pj = Fraction of annual rainfall events that produce runoff (assumed 90%, 

although not necessarily true for western Washington storm intensities) 

Rv = Runoff coefficient 

Rv = 0.05 + 0.9Ia 

Ia = Percent impervious cover 
Stillaguamish Fecal and DO TMDL Submittal Report Page D-185 

Table D-1. Mean concentration estimates and percent imperviousness for various land uses. 

Fecal 

coliform 

Total 

phosphorus BOD5

Impervious 

Land use type cover 

(cfu/100mL) (mg/L) (mg/L) (%) 

Roadway 890 0.26 10 80 

Residential 2000 0.26 13 40 

Commercial/Urban 980 0.21 15 87 

Forest 100 0.10 1 20 

Agriculture 3000 0.35 15 30 

Table D-2. Land use assumptions for individual sub-basins as percentages. 

Sub-basin Roadway Residential Commercial Forest Agriculture 

Glade Bekken 2% 11% 0.4% 72% 16% 

Pilchuck Creek 4% 2% 0.4% 80% 2% 

Portage Creek at 43rd 13% 35% 10% 24% 13% 

Fish Creek 2% 15% 3% 70% 10% 

Portage Creek at 212th 8% 26% 6% 39% 23% 

Armstrong Creek 1% 6% 1% 77% 13% 

Harvey Creek at Grandview 0.3% 0.1% 0% 99.6% 0% 

Kackman Creek at 252nd 1% 8% 0% 69% 13% 

March Creek 3% 15% 5% 0% 78% 

Lower S.F. Stillaguamish 2% 19% 2% 44% 32% 

Lower N.F. Stillaguamish 0.7% 1.5% 0.5% 85% 12% 

Lake Martha Creek 2.2% 18.5% 0.1% 73% 0% 

Unnamed Creek #0456 1.6% 17% 0% 82% 0% 

Warm Beach Dike Pond 1.4% 6.2% 0.4% 76% 16% 

Areas

Glade Bekken (2000 acres) 

Pilchuck (48,768 acres) 

Portage at 43rd (5550 acres) 

Fish (4813 acres) 

Portage at 212th (13,696) 

Armstrong (7145 acres) 

Harvey (600 acres) 

March (800 acres) 

Lower South Fork (15,617 acres) 

Lower North Fork (30,567 acres) 

Martha (1350 acres) 

Unnamed (900 acres) 

Warm Beach (2590 acres) 
Page D-186 Stillaguamish Fecal and DO TMDL Submittal Report

Table D-3. Example of Wasteload Allocation Calculation for BOD 

 

Portage Creek at 212th (Table 37, page 111) 

 

13696 Acres 

Estimated total area draining to this part of Portage 

Creek 

 Road Residential Commercial Forest Agriculture 

 

A = Acres 1095.68 3560.96 821.76 5341.44 3150.08 

Land Use 0.08 0.26 0.06 0.39 0.23 

C = BOD mg/L 10 13 15 1 15 

 

1. Calculate R (annual runoff in inches) 

 

R=P x Pj x Rv 

Ia is a similar value to Rv, so Ia was substituted for 

Rv 

 

P = Annual rainfall = 46.5 inches 

Ia 0.81 0.42 0.89 0.22 0.33 

Rv 0.779 0.428 0.851 0.248 0.347 

R 33.8985 17.577 37.2465 9.207 13.8105 

 

2. Calculate total load for each land use type 

 

L = 0.226 x R x C x A 

L 83941 183892 103760 11114 147479 

Total Load 530187 lbs.per year 1453 lbs per day 

% of Total Load 15.83% 34.68% 19.57% 2.10% 27.82% 

 

3. Determine loading capacity for BOD based on similar reduction required for fecal coliform 

bacteria 

 

Fecal coliform reduction required for this location was 147 (GM) to 25 (Target GM) = 

83% 

reduction 

Using an 80% reduction for BOD, it would 

be 1453 lb per day reduced to a target BOD load of 291 lb per day 

For this calculation, 291 lb per day was rounded to 300 lb per day loading capacity 

 

4. Determine loading of BOD from background sources (undetermined) 

Assume values of 1.2 mg/L BOD from all land use types except Agriculture, assumed 3 mg/L BOD 

 

 Road Residential Commercial Forest Agriculture 

A = Acres 1096 3561 822 5341 3150 

Land Use 0.08 0.26 0.06 0.39 0.23 

C = BOD mg/L 1.2 1.2 1.2 1.2 3 

L 10073 16975 8301 13337 29496 
Stillaguamish Fecal and DO TMDL Submittal Report Page D-187 

Table D-3. Example of Wasteload Allocation Calculation for BOD 

 

Portage Creek at 212th (Table 37, page 111) 

Total Background 

Load 78181 lbs per year 214 lbs per day 

 

For this 

calculation, 214 rounded to 210 lbs per day 

5. Determine loads from roadways to calculate WLAs; road drainage systems are under Stormwater Permits 

Load from roadways based on 8% of 300 lb per day loading capacity 

24 lb/day rounded to 20 lb 

per day 

6. Determine loads from Nonpoint Sources by Subtraction 

 Loading Capacity = Background LA + NonPoint LA + Roadways WLA 

300 = 210 + Nonpoint LA + 20 

Nonpoint LA = 70 lb/ day 

7. Determine Snohomish County and WSDOT portions of roadways Wasteload 

Allocation 

 

Relative acreages of roadways under county jurisdiction vs. WSDOT jurisdiction was used 

to calculate allocations of 12 lb/day to Snohomish County and 8 lb/day to WSDOT, out of a total of 20 

lb/day 

(Roadways: Snohomish County = 27% & WSDOT = 16.7%) 
Page D-188 Stillaguamish Fecal and DO TMDL Submittal Report
Stillaguamish Fecal and DO TMDL Submittal Report Page E-189 

Appendix E. 

Watershed Projects Already Implemented by 

Local Organizations 
Page E-190 Stillaguamish Fecal and DO TMDL Submittal Report
Stillaguamish Fecal and DO TMDL Submittal Report 

Table E-1. Recent City of Arlington Projects Addressing Impaired Waters in Stillaguamish Watershed Project Title River Segment Parameter 

Addressed 

Organization Date Started/ 

Completed 

Public Education Signs at arterial-stream crossings Portage Cr General City of 

Arlington 

2002 Obje

qual

Provide contact information for enforcement at task force projects 

 Temperature SSFETF, City 

of Arlington 

2003 

“Arlington Update” newsletter articles on water quality programs and actions 

All basins in city limits 

General City of 

Arlington 

Quarterly 

“Arlington Times” newspaper articles on watershed subjects 

All basins in city limits 

General City of 

Arlington 

 Regu

supp

Storm drain stenciling All basins in city 

limits 

Dissolved Oxygen 

City of Arlington 

 “Du

Strea

Watershed Protection program at airport and industrial center 

Portage Cr (also Quilceda) 

Temperature, Dissolved Oxygen 

City of Arlington 

2003 Enga

good 

Research and inspection of all septic systems at the airport 

Portage creek springs 

Ground water City of 

Arlington 

1998-2000 Goo

and 

Participated in the Portage Creek Stewardship program 

Portage Cr Temperature, 

Dissolved Oxygen 

City of Arlington 

January – May 2003 

Inclusalva

Public Participation Began operation of new state of the art Wastewater Treatment plant 

All city, other than areas served by Marysville 

Dissolved Oxygen, Fecal Coliform, BOD, COD 

City of Arlington 

1997 Man

methfeca

Golf course ponds water quality improvements 

Prairie Cr Temperature, 

Dissolved Oxygen, Nutrients 

Gleneagle golf course, High School VoTech, City of Arlington 

 Man

wateSchoplan

March Creek water quality investigation 

March Cr Fecal 

Coliform, Dissolved Oxygen, 

City of Arlington, landowners 

 Coo

moninstapollu
Page E-192 Stillaguamish Fecal and DO TM

Project Title River Segment Parameter 

Addressed 

Organization Date Started/ 

Completed 

Public Education 

Temperature, Nutrients 

alter

Citizen Advisory Committee on Stormwater 

All basins in city limits 

General City of 

Arlington 

Ongoing Educ

Planning and Development NPDES Phase II application All basins in city 

limits 

General City of 

Arlington 

2003 On-t

SCD Annexation General City of 

Arlington 

2003 Ann

Con

Adopted new Critical Areas regulations 

All basins in city limits 

Temperature, Dissolved Oxygen 

City of Arlington 

2003 Buff

habi

Significant tree rules All basins in city 

limits 

Temperature City of 

Arlington 

 Enco

Low Impact Development All basins in city 

limits 

Water Quantity 

City of Arlington 

 Enco

viab

Developed strict TESC standards All basins in city 

limits 

Sediment City of 

Arlington 

 Requ

NPDEnfo

Identified Priority Protection Areas All basins in city 

limits 

Temperature, Dissolved Oxygen 

City of Arlington 

 Dev

EcolcharidenwetlstreaE-2) 

Enforcement Enforce TESC standards All basins in city 

limits 

Sediment City of 

Arlington 

Ongoing Cod

cons

Construction project turbidity monitoring 

All basins in city limits 

Sediment City of 

Arlington 

 Man

probTurb

Operations and Maintenance Gleneagle pet waste station Prairie Cr Fecal City of First 
Stillaguamish Fecal and DO TMDL Submittal Report 

Project Title River Segment Parameter 

Addressed 

Organization Date Started/ 

Completed 

Public Education 

Coliform Arlington used 

Prairie Creek Storm Detention System Cleaning 

Prairie Cr General, 

Water Quantity 

City of Arlington 

2004 Rest

flowand 

Riparian Restoration Numerous stream and wetland restoration projects (see attached Table A-2) 

All basins in city limits 

Temperature, Dissolved Oxygen 

City of Arlington 

 Tota

mosresto

Provided trees to landowners willing to plant along critical areas 

City wide Temperature, 

Dissolved Oxygen 

City of Arlington 

Ongoing Estim

Supplemental plantings and maintenance in existing riparian restoration projects 

City wide Temperature, 

Dissolved Oxygen 

Banksavers, City of Arlington 

Ongoing Estim

Prisoner crew plantings—new plus follow-up maintenance 

City wide Temperature, 

Dissolved Oxygen 

Oscar Cullem, City of Arlington 

Ongoing 5 acr

Portage Creek ponds vegetation enhancement 

Portage Creek Temperature, 

Dissolved Oxygen 

Pioneer Museum, City of Arlington 

2003/4 Add

pondhisto

Golf course plantings near ponds Temperature, 

Dissolved Oxygen 

Gleneagle golf course, High School VoTech, City of Arlington 

2003/4 Also 

Wetland Creation / Acquisition Eagle Creek elementary school wetland creation 

Eagle Cr Temperature, 

Nutrients 

City of Arlington 

 3 acr

Pioneer elementary school wetland creation 

Prairie Cr Temperature, 

Nutrients 

City of Arlington 

 6 acr

Monitoring Illicit discharge detection and elimination 

 Fecal 

Coliform, Dissolved 

City of Arlington 

 e.g., 

insp
Page E-194 Stillaguamish Fecal and DO TM

Project Title River Segment Parameter 

Addressed 

Organization Date Started/ 

Completed 

Public Education 

Oxygen 

Increase water quality staffing General City of 

Arlington 

 New 

May 

Continuous water quality monitoring stations 

Portage Cr, Prairie Cr 

Temperature, Dissolved Oxygen 

City of Arlington 

 Hyd

instayet t

Stormwater outfall monitoring Largest 

stormwater outfall; discharge to mainstem Stilly 

Fecal Coliform, Dissolved Oxygen, Temperature 

City of Arlington 

September 2003 Main 

backmon

Source water monitoring Mainstem Stilly Temperature, 

Turbidity, pH, Conductivity, Water Quantity 

City of Arlington 

 Dail

Dep

Wastewater NPDES compliance effluent monitoring 

Mainstem Stilly Fecal 

Coliform, Dissolved Oxygen, Temperature 

City of Arlington 

Wastewater additional effluent monitoring 

Mainstem Stilly Total 

Phosphorus, Total Kjeldahl Nitrogen 

City of Arlington 

March Creek water quality investigation 

March Cr Fecal 

Coliform, Dissolved Oxygen, Temperature 

City of Arlington 

 Map

sampand alterdeficstormPubl

Support tribal monitoring programs Portage Cr Fecal 

Coliform 

Stillaguamish Tribe, City of 

 Field 

Bact
Stillaguamish Fecal and DO TMDL Submittal Report 

Project Title River Segment Parameter 

Addressed 

Organization Date Started/ 

Completed 

Public Education 

Arlington gene

detewill iden

Construction project turbidity monitoring 

All basins in city limits 

Sediment City of 

Arlington 

 Man

probTurb
Page E-196 Stillaguamish Fecal and DO TM

Table E-2. 2002-2004 Stillaguamish BankSavers Riparian Planting in Stillaguamish Watershed (Stillaguamish Tribe) Site Identifier Linear ft Miles

Avg. Buffer 

Width Acreage

# of 

Plants Water Body Project Pa

A 1650 30 1.1 1234 Unnamed trib to NF Stilly Snohomish B 1200 20 0.6 503

Glade Bekken (Trib to Lower Stilly) Snohomish 

C 15650 50 18.0 2161 Old Stilly Channel 

Max AlbertProject 

D 600 15 0.2 500 Stilly Mainstem None E 1500 50 1.7 2059 Stilly Mainstem None F 1854 6.0 2500 Pilchuck Creek CREP projG 1300 50 1.5 2005 Church Creek 

Snohomish Jacobson 

H 3320 25 1.9 326 Church Creek trib 

Snohomish Jacobson 

I 300 30 0.2 505 Church Creek trib 

Snohomish Jacobson 

J 1300 45 1.3 130 Old Stilly Channel 

Max AlbertProject 

K 400 60 0.6 110 Old Stilly Channel 

Max AlbertProject 

L 945 40 0.9 562 Stilly Mainstem None M 2660 20 1.2 1426 Unnamed trib to NF Stilly Stilly-SnohN 2000 80 3.7 1332 Old Stilly Channel CREP projO 1039 4.3 1487 Stilly Mainstem CREP projP 1800 300 12.4 1300 NF Stilly @ C-Post Bridge Stilly Tribe Q 600 20 0.3 500 Trib to NF Stilly Snohomish R 3500 30 2.4 1700

Harvey Creek/Kackman Creek Snohomish 

Totals for all projects 41618 7.9 58.3 20340
Stillaguamish Fecal and DO TMDL Submittal Report 

Table E-3. Portage Creek Watershed Revegetation Sites - The BankSavers Project (Stillaguamish Tribe) 

# of 

Plants 

# of 

Plants Acres 

Site # Planted

 to be 

Planted

Maintenance 

Services Protected

Length of Project

Avg. Buffer Width/Fencing 

Installed Project Pa

1 2450.0 Yes 2.2 3200 ft 30 ft/4400 ft 2 2260.0 Yes 1.9 4150 ft 20 ft 3 3500 Yes 2.3 2000 ft 50 ft 

Snohomish grant 

4 594.0 Yes 0.6 1300 ft 20 ft 5 4962.0 Yes 3.3 7110 ft 20 ft 6 1099.0 Yes 1.1 1200 ft 40 ft Stilly Tribe 7 3576.0 Yes 3 

Snohomish Force 

8 1365.0 Yes 1.5 1200 ft 60 ft Stilly-Snoh9 4611.0 Yes 3 2600 ft 50 ft Stilly Tribe 

10 889.0 Yes 1.4 3000 ft 20 ft 11 Yes 2.1 3000 ft 30 ft Stilly Snoh12 200.0 Yes 1.1 2000 ft 25 ft Stilly Snoh13 200.0 Yes 0.6 500 ft 50 ft Stilly Snoh14 270.0 2300 Yes 3.5 5100 ft 30 ft Stilly Snoh

Totals 22476.0 5800 27.5

36360 (6.9 miles) 20 to 60/4400 ft 
Page E-198 Stillaguamish Fecal and DO TMDL Submittal Report

Table E-4. Recent Snohomish County/Partner Projects Addressing Impaired Waters in 

Stillaguamish Watershed 

Project Title River Segment Parameter 

Addressed 

Organization Date 

Started/ 

Completed 

 Pilchuck Creek 

Trib80a 

 Stillaguamish Tribe 

Streambank 

Revegetation 

(many individual 

projects) 

Indian, Church, Deer, 

Deforest, French, 

Jim, Jorgenson 

Slough, Portage, 

Porter, Prairie, Riley, 

Rock, Sills, Trafton 

II 05-0145 

Temperature City of 

Arlington/Stillaguamish Tribe, 

Snohomish Conservation 

District, Stilly-Snohomish 

Fisheries Enhancement Task 

Force, Stillaguamish Flood 

Control District, WDFW, 

DNR, private landowners, 

Snohomish County 

1994 - 2004 

Flow 

Enhancement 

Structure 

Old Stillaguamish 

Channel 

Temperature, 

Dissolved Oxygen 

Stillaguamish Flood Control 

District, Stillaguamish Tribe 

2003 

Riparian Repair/ 

Revegetation 

South Fork, Church, 

Portage, Kackman, 

North Fork, Trib to 

North Fork near 

Trafton, Trib to 

South Fork off Burn 

Rd 

Temperature, some 

Fecal Coliform 

locations 

Snohomish County 2001-2004 

Glade Bekken 

restoration 

Glade Bekken 

watershed 

Temperature, 

Dissolved oxygen, 

Fecal coliform 

Snohomish County 1996-2001 

Ambient 

monitoring 

8 sites on mainstem 

and tributaries 

Temperature, 

Dissolved oxygen, 

Fecal coliform 

Snohomish County 1994-

ongoing 

Water quality 

complaint 

investigations 

Clean Water District Temperature, 

Dissolved oxygen, 

Fecal coliform 

Snohomish County 1994-

ongoing 

Church Creek 

restoration 

Church Creek 

watershed 

Temperature, 

Dissolved oxygen, 

Fecal coliform 

Snohomish County 2000-

ongoing 

Dry Weather 

Outfall 

Monitoring 

Clean Water District Temperature, DO, 

Fecal Coliform 

Snohomish County 1998-

Ongoing 

Adult Education 

(e.g. Watershed 

Keepers, tours, 

community 

events) 

Clean Water District Temperature, DO, 

Fecal Coliform 

Snohomish County 1994 – 

ongoing 

Streamside 

Landowner 

Workshops 

Clean Water District Temperature, DO, 

Fecal Coliform 

Snohomish County with 

Ecology funding 

2003 - 2004 

Streamside BMP 

Direct Mail 

campaign 

Stillaguamish Basin Temperature, DO, 

Fecal Coliform 

Snohomish County with 

Ecology funding 

2004 

Teacher and 

Youth Education 

Most schools in 

CWD 

Temperature, DO, 

Fecal Coliform 

Snohomish County 1996 - 

ongoing 
Stillaguamish Fecal and DO TMDL Submittal Report 

Table E-5. Snohomish Conservation District: 2004 Public Education Projects in Stillaguamish Watershed 

Project Title River Segment Parameter 

Addressed

Organization Date 

Started/ 

Completed

Spring Farm Clinic Lower 

watershed 

General Snohomish CD 4/24/04 Held 

Ice Cream Social Lower 

watershed 

General Snohomish CD 6/18/04 Held 

Arlin

Silvana Fair (booth) Lower 

watershed 

General Snohomish CD 7/31/04 At Sil

Stanwood-Camano Fair (booth) Lower 

watershed 

General Snohomish CD 8/6-8/8/04 In Sta

Festival of the River (booth) Lower 

watershed 

General Snohomish CD 8/6/04 In Ar

Fall Farm Workshop Lower 

watershed 

General Snohomish CD 10/9/04 At Sta

Table E-6. Snohomish Conservation District: 2004 Projects in Stillaguamish Watershed 

Project Type River Segment Project Type River SSite visit/farm plan review Arlington Junction 

South 

Planting/site visit/Nutrient management Hat Slou

Site visit/farm plan review Arnot Road 

Drainages 

Data collection & Evaluation/Meetings/Site visit/farm plan review 

Hell-Ha

Site visit/farm plan review Boulder Ridge Data Collection & Evaluation/ Nutrient 

Management/Site visit/farm plan review 

Higgins 

Fencing & Structural BMPs/Site visit/farm plan review 

Burn Hill Road Drainages 

Firebreak/Structural BMPs/Site visit/farm plan assistance 

Jackson 

Site visit/farm plan review Church Creek Structural BMPs/Site visit/farm plan 

review 

Jim Cre

Site visit/farm plan review Deer Creek Nutrient management/Fencing/ Site 

visit/farm plan review 

Jordan R

Brush Management/Structural Ebey Hill Drainages Data Collection & Evaluation/Fencing/ Kackma
Page E-200 Stillaguamish Fecal and DO TM

Project Type River Segment Project Type River SBMPs/Site visit/farm plan review Site visit/farm plan review Data collection/Site visit/farm plan review 

Frailey Mountain Drainages 

Structural BMPs/Data Collection & Evaluation/ Site visit/farm plan review/Nutrient management/Brush management 

Pilchuck 

Site visit/farm plan review/Data collection, Structural BMPs/Tree & shrub establishment 

Glade Bekken Fencing/ Site visit/farm plan review Silvana 

Fund raising/ Site visit/farm plan review 

Grandview Area Site visit/farm plan review Squire C

Data Collection/Fencing/Site visit/farm plan review 

Harvey Armstrong Creek 

Structural BMPs/Data Collection & Evaluation/ Site visit/farm plan review/Nutrient management/Brush management/Pest management 

Stillagua
Stillaguamish Fecal and DO TMDL Submittal Report Page F-201 

Appendix F. 

NPDES Permitted Facilities in Stillaquamish 

Watershed 
Page F-202 Stillaguamish Fecal and DO TMDL Submittal Report
Stillaguamish Fecal and DO TMDL Submittal Report 

Table F-1. NPDES permitted facilities in Stillaguamish Basin with active permits that discharge directly to surface water. Facility Name Facility Type Permit Type Permit ID Limited Parameters Kwant Dairy Farm General WAG013025B WA DFW Arlington Hatchery 

Fish General WAG133009D Total residual chlorine, flow, settleable 

suspended solids 

WA DFW Whitehorse Ponds 

Fish General WAG133008D Total residual chlorine, flow, settleable 

suspended solids 

CMS 300 St Pit Industrial General WAG503285C Oil and grease, pH CUZ Concrete Products Inc 

Industrial General WAG503338B Oil and grease, pH, total dissolved soli

Green Crow Corp. Industrial General WAG503358B Oil and grease, pH Lenz Enterprises Industrial General WAG503069C Oil and grease, pH Rinker Materials Arlington Pit 

Industrial General WAG503058C Oil and grease, pH 

Rinker Materials BNI Pit Industrial General WAG503317C Oil and grease Smokey Point Concrete Industrial General WAG503088C Oil and grease, pH Stanwood Redi Mix Inc Industrial General WAG503212C Oil and grease, pH