Coastal Pathogen TMDLs

Fecal indicator bacteria measurements are used to assess the presence of fecal waste material in a waterbody.  E. coli and enterococci bacteria are commonly measured as indicators of fecal waste.  The presence of fecal waste material is correlated with the potential presence of illness-causing pathogens, such as bacteria, viruses, or protozoa, which can cause illness either through direct contact or incidental water ingestion, impacting the contact recreation beneficial use (REC-1) or through ingestion of contaminated shellfish (SHELL).

The 2012 Section 303(d) list identifies thirteen (13) freshwater streams in the North Coast Region as impaired for the water contact recreation (REC-1) beneficial use due to exceedances of fecal indicator bacteria criterion.  The 2012 Section 303(d) list also identifies twelve (12) ocean beaches as impaired for SHELL beneficial use due to concentrations of fecal indicator bacteria.  Development of a Total Maximum Daily Load (TMDL) is required under Section 303 of the Clean Water Act to address waterbody-pollutant pairs that are identified on the 303(d) list of impaired waters.

The North Coast Regional Water Quality Control Board (Regional Water Board) approved by Resolution No. R1-2015-0012 the 2014 Triennial Review of the Water Quality Control Plan for the North Coast Region (Basin Plan), including a list of Basin Planning Project Priorities. TMDL development was identified as the Region’s number one planning priority, with the Ocean Beaches and Freshwater Streams Pathogen TMDL listed as priority #1c.

The development of a TMDL generally follows a common analytical process, including but not limited to: confirmation of impairment, assessment of pollutant sources and/or factors contributing to the impairment, and an assessment of the source reductions necessary to achieve water quality objectives and protect beneficial uses. Freshwater stream impairments are being investigated and assessed under the Coastal Streams Pathogen TMDL Project and the ocean beaches conditions are being addressed by the Ocean Beaches Pathogen TMDL Project

Analytes of Interest

The Regional Water Board collected water samples to assess the potential for recreational users of a given waterbody to come in contact with pathogens.  These water samples were measured for E. coli, total coliform, and enterococci fecal indicator bacteria. Bacteroides bacteria DNA markers are another useful measurement that was conducted on the collected water samples.  Bacteroides bacteria are animal host-specific, thereby allowing the assessment of the source of fecal waste that may be associated with elevated fecal indicator bacteria concentrations.  In the Coastal Streams Pathogen TMDL Project, animal host-specific bacterial source DNA markers may be used as a line of evidence when assessing the likely sources of fecal indicator bacteria in surface water samples.  Animal-host DNA markers measured were the overall DNA and animal host specific markers for humans, dogs, birds and ruminants (e.g., cows and deer).  Assessment of these data are underway.  Results will be posted once monitoring reports are final.

Coastal Streams Pathogen TMDL Project

Seven (7) of the freshwater streams listed as impaired due to pathogens on the 2012 Section 303(d) list are found within the Russian River Watershed and will be addressed by the Action Plan for the Russian River Watershed Pathogen TMDL, once adopted.  Of the six (6) remaining streams listed for pathogen impairment in the North Coast Region, one stream, Pudding Lagoon, is being evaluated together with Pudding Beach as part of the Ocean Beaches Pathogen TMDL Project.  The remaining five (5) streams, listed in the following table and depicted on attached map, will be addressed in this Coastal Stream Pathogen TMDL Project.

  Coastal Streams Pathogen TMDL Project Impaired Streams
  Hydrologic Unit   Listed Water Body Name
  Trinidad   Little River
  Mad River   Norton Creek
  Eureka Plain   Jolly Giant Creek
  Gannon Slough
  Lower Elk River and Martin Slough

Impaired Streams Monitoring Study

sampling Little River
Cameron Hayvaert, member of the Watershed Stewardship Program, collecting water samples for fecal indicator bacteria analysis from the Little River in Humboldt County. Photo credit Jennifer Kalt of Humboldt Baykeeper

Five impaired streams were evaluated under the Coastal Stream Pathogen TMDL Project through monitoring of fecal indicator bacteria to verify water quality conditions and compare to water quality objectives.  The temporal variability of fecal indicator bacteria in these Section 303(d) listed streams was measured near the mouth of the catchments to determine water column concentrations under both wet and dry climatic conditions. Assessment of these data will provide the foundation for source reductions that may be needed to achieve water quality objectives, which fully support beneficial uses in these waters.  Bacteroides bacteria markers analyzed in conjunction with the fecal indicator bacteria samples collected from the impaired streams will also be used to assist staff’s evaluation of possible sources where elevated fecal indicator bacteria levels are detected.

Source Assessment Monitoring Study

Cameron Hayvaert, member of the Watershed Stewardship Program, collecting water samples for fecal indicator bacteria analysis from cattle pasture runoff. Photo credit Jennifer Kalt of Humboldt Baykeeper

The Porter-Cologne Water Quality Control Act directs Regional Water Boards to develop programs of implementation to achieve water quality objectives, which for the purposes of the TMDL Program generally are established as Action Plans, permits, or third party programs. As an example, many of the counties in the North Coast Region are developing Local Area Management Plans (LAMPs) as allowed under the statewide Water Quality Control Policy for Siting, Design, Operation, and Maintenance of Onsite Wastewater Treatment Systems (OWTS Policy), which may be sufficient as third party programs to address the OWTS source category in some or all of the listed waters.

To establish a pollutant control program or Action Plan capable of returning an impaired water to a trajectory of recovery, it is necessary to identify the sources of the pollutant. A pathogen source study endeavors to determine the degree to which known categories of fecal waste discharge (e.g., cattle pastures, septic systems, urban runoff, or wildlife areas) are in fact a significant source in a given waterbody. This is typically accomplished by collecting ambient water quality data immediately downstream of suspected source locations during both dry and wet periods. The suspected source locations sampled are listed in the following table and depicted on attached map.

  Locations Sampled near Suspected Fecal Waste Sources
  Suspected Source Category   Stream Name   Sampling Location
  Cattle Pastures   Roadside Ditch   Jackson Ranch Road
  Roadside Ditch   Foster Road
  Elk River   Zanes Road
  Salmon Creek   Hookton Road
  Swain Slough   Elk River Road
  Liscom Slough   Jackson Ranch Road
  Unnamed Slough   Lamphere Road
  Septic Systems   Mill Creek   Stagecoach Road
  Strawberry Creek   Highway 101
  Unnamed Stream   Anker Road
  Freshwater Creek   Freshwater Park
  Jacoby Creek   Old Arcata Road
  Sewered Areas   Cooper Gulch   Myrtle Ave
  Grotzman Creek   Bayside Road
  Campbell Creek   7th Street
  Campbell Creek   14th Street
  McDaniel Slough   Q Street
  Martin Slough   Campton Road
  Wildlife Areas   Graham Gulch   Pacific Lumber Camp Road
  Hookton Slough   Hookton Road
  Jacoby Creek   Jacoby Creek Road
  Elk River, S.F.   Cattail Creek
  Unnamed Slough   Hunt Creek Station
  Unnamed Slough   Visitor Center
  Unnamed Slough   Long Pond

Reference Streams Monitoring Study

Jeremiah Puget, Regional Water Board staff, collecting water samples for fecal indicator bacteria analysis from Clarks Creek in Del Norte County. Photo credit Steve Butkus.

In conjunction with Coastal Stream Pathogen Project, Regional Water Board staff collected data assessing FIB levels from sixteen (16) reference system stream catchments in the North Coast Region. A “reference system” is a stream catchment that is minimally impacted by human activities that could affect indicator bacteria levels in streams. The Regional Water Board collected samples to assesses bacteria levels from sixteen (16) reference stream catchments, which are listed in the table and depicted on the attached map.

  Reference Stream Sampling Locations
  Hydrologic Unit   Stream Name   Location
  Smith River   Cedar Creek   Jedediah Smith State Park
  Clarks Creek   Jedediah Smith State Park
  Mill Creek   Jedediah Smith State Park
  Redwood Creek   Prairie Creek   Prairie Creek Redwoods State Park
  Lost Man Creek   Redwood National Park
  Little Lost Man Creek   Redwood National Park
  Eel River   Cow Creek   Humboldt Redwoods State Park
  Calf Creek   Humboldt Redwoods State Park
  Harper Creek   Humboldt Redwoods State Park
  Albee Creek   Humboldt Redwoods State Park
  Mill Creek   Humboldt Redwoods State Park
  Little Mill Creek   Humboldt Redwoods State Park
  Mendocino Coast   Phillips Gulch   Salt Point State Park
  Miller Creek   Salt Point State Park
  Stockhoff Creek   Stillwater Cove Regional County Park
  Freezeout Creek   Willow Creek State Park

Project Documents

The Coastal Streams Pathogen TMDL Project is intended to result in a plan for the assessment and control of fecal waste sources in the coastal streams listed as impaired for pathogens.  In accordance with the Health and Safety Code, any regulation that relies on science as its basis must be reviewed by a panel of scientific peers.  The results of the scientific work conducted under the Coastal Streams Pathogen TMDL Project will be posted on this webpage following successful completion of thescientific peer review process.

Project Milestones and Timeline

The development of a Coastal Stream Pathogen TMDL includes the following project milestones and timeline as follows:

  Project Milestones and Timeline
  Milestone   Date   Status
  Quality Assurance Project Plan   November 2015   Complete
  Data Collection   2016-2018   Complete
  Data Assessment and Analysis   2018   In Progress
  Peer Review Staff Report   2019   Future
  Public Review Draft Staff Report, Action Plan, & BPA   2019   Future
  Region Water Baord Adoption Hearing   2020   Future
  State Board Adoption Hearing   2021   Future
  EPA Approval   2022   Future



Ocean Beaches Pathogen TMDL Project


Emily McClintock, member of the Watershed Stewardship Program collecting water samples for fecal indicator bacteria analysis from the Stillwater Cove in Sonoma County. Photo credit Steve Butkus

Potential for human pathogen exposure has been linked to impairment of the shellfish consumption (SHELL) designated beneficial use, which is defined as water suitable for the collection of filter-feeding shellfish (e.g., clams oysters, and mussels, but not crabs) for human consumption. The 2012 Section 303(d) list identifies twelve (12) North Coast ocean beaches as impaired for the SHELL beneficial use due to the potential for pathogen exposure.

The North Coast Regional Water Quality Control Board conducted a monitoring study to assess pathogen levels and possible fecal waste sources at the ocean beaches listed as impaired in 2012, shown in the table below and depicted on the attached map. The project included analysis of E. coli, total coliform, and enterococci fecal indicator bacteria. Additionally, in order to assess potential waste sources, host specific bacterial markers for general, human, ruminant, dog, and birds were used to quantify the origins of the Bacteroides bacteria in each water sample.


  Ocean Beaches Pathogen TMDL Project Impaired Beaches
  Hydrologic Unit   Listed Water Body Name
  Trinidad   Trinidad State Beach
  Old Home Beach
  LuffenHoltz Beach
  Moonstone County Park
  Clam Beach (near Strawberry Creek)
  Mad River   Clam Beach (near Mad River Mouth)
  Mendocino Coast   MacKerricher State Park (near Virgin Creek)
  Pudding Beach
  Hare Beach
  Caspar Headlands State Beach
  Big River Beach at Mendocino Bay
  Bodega   Campbell Cove

Project Documents

The Ocean Beaches Pathogen TMDL Project is intended to result in a plan for the assessment and control of fecal waste sources in the coastal beaches listed as impaired for pathogens. In accordance with the Health and Safety Code, any regulation that relies on science as its basis must be reviewed by a panel of scientific peers. The results of the scientific work conducted under the Ocean Beaches Pathogen TMDL Project will be posted on this webpage following successful completion of the scientific peer review process.

Project Milestones and Timeline

The development of the Ocean Beaches Pathogen TMDL includes the following project milestones and timeline as follows:

  Project Milestones and Timeline
  Milestone   Date   Status
  Quality Assurance Project Plan   November 2015   Complete
  Data Collection   2016-2018   Complete
  Data Assessment and Analysis   2018   In Progress
  Peer Review Staff Report   2019   Future
  Public Review Draft Staff Report, Action Plan, & BPA   2019   Future
  Region Water Baord Adoption Hearing   2020   Future
  State Board Adoption Hearing   2021   Future
  EPA Approval   2022   Future

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