Coastal Pathogen Project

Fecal indicator bacteria (FIB) measurements are used to assess the presence of fecal waste material in a waterbody.  Escherichia coli (E. coli) and enterococci bacteria are commonly measured as these 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).

In response to the 2012 listings, the North Coast Regional Water Quality Control Board (Regional Water Board) identified the Ocean Beaches and Freshwater Streams Pathogen Project as a Basin Planning Priority during the 2014 Triennial Review process. The development of a TMDL or correlated study project generally follows a common analytical process that may include but is not limited to confirmation of impairment, assessment of pollutant sources and/or factors contributing to the impairment, or an assessment of the source reductions necessary to achieve water quality objectives and protect beneficial uses. For this project freshwater stream impairments were investigated and assessed under the Impaired Streams Monitoring Study of the Coastal Pathogen Project. Ocean beaches conditions were considered in conjunction with the Ocean Beaches Monitoring Study of the Coastal Pathogen Project.

Impaired Streams Monitoring Study

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 under the Action Plan for the Russian River Pathogen TMDL.  The remaining six (6) streams, listed in the following table, are considered under the Impaired Streams Monitoring Study of this Coastal Pathogen Project.

The locations from where samples were collected for the Impaired Streams Monitoring Study are shown in the figure below.

A map of the locations from where samples were collected for the Impaired Monitoring Study from six impaired streams in Humboldt County

Six impaired streams were evaluated under the Impaired Streams Monitoring Study of the Coastal Pathogen Project through monitoring of FIB 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 provide the foundation to identify source reductions that may be needed to achieve water quality objectives and protect beneficial uses.  Microbial Source Tracking (MST) markers, discussed in more detail below, were analyzed in conjunction with the FIB samples and will also be used to assist staff’s evaluation of possible sources that may require control.

Ocean Beaches Pathogen TMDL Project

Potential for human pathogen exposure has been linked to impairment of 1) 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, and 2) the water contact recreation (REC-1) designated beneficial use, which is defined as water suitable for recreational activities involving body contact with water, where ingestion of water is reasonably possible. 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. Four (4) of the twelve (12) ocean beaches that are impaired for SHELL beneficial use are also impaired for REC-1 beneficial use.

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. The project included analysis of E. coli, total coliform, and enterococci fecal indicator bacteria. Additionally, in order to assess potential waste sources, host specific MST bacterial markers for general, human, ruminant, dog, and birds were used to quantify the origins of the fecal indicator bacteria in each water sample.

The locations from where samples were collected for the Ocean Beaches Monitoring Study from impaired beaches in Humboldt County, Mendocino County, and Sonoma County are shown in the three figures below.

A map of the locations from where samples were collected for the Ocean Beaches Monitoring Study from six impaired beaches in Humboldt County

A map showing the locations from where samples were collected for the Ocean Beaches Monitoring Study from five impaired beaches in Mendocino County

A map showing the location from where samples were collected for the Ocean Beaches Monitoring Study from one impaired beach in Sonoma County

Pollutant Sources Assessment

Source Assessment Study

Cameron Hayvaert, member of the Watershed Stewardship Program, collecting water samples 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 may be 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) 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 waters where OWTS could be identified as a potential pollutant source.

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, OWTS, 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 during both dry and wet periods. The suspected source locations sampled in conjunction with the Coastal Pathogen Project are listed in the following table.

¹Not included in analysis due to insufficient number of samples

The locations from where samples were collected for the Source Assessment Study from streams in the northern and southern Humboldt Bay areas are shown in the two figures below.

A map showing the locations from where samples were collected for the Source Assessment Study from northern Humboldt Bay area.

A map showing the locations from where samples were collected for the Source Assessment Study from southern Humboldt Bay area

Microbial Source Tracking (MST)

To augment water samples measured for E. coli, total coliform, and enterococci fecal indicator bacteria, Regional Water Board staff collected MST markers, another useful measurement applied to the water samples collected for this project.  MST markers are animal host-specific, thereby providing information about the source of fecal waste that may be associated with elevated fecal indicator bacteria concentrations.  Under the Coastal Pathogen Project, animal host-specific MST markers are used as one line of evidence when assessing the likely upstream sources of fecal indicator bacteria in surface water samples.  MST markers measured include animal host specific markers for humans, dogs, birds and ruminants (e.g., cows and deer). 

Land Cover and Land Use

Regional Board Staff are assessing the land cover as well as land use patterns within the watersheds of each of the streams and beaches sampled under the various studies of the Coastal Pathogen Project. These assessments will provide two lines of evidence to identify potential upstream sources contributing to fecal pollution in these waterbodies. Land cover data will be derived from the 2012 United States Department of Agriculture Cropland Data Layer and will provide coverage of land cover categories of interest such as agriculture, forests, grasslands, and urban/developed areas in the watersheds being assessed. Land use data will be derived from the most recent publicly available county parcel data and will provide the prevalence of land use categories of interest such as developed-sewered, developed-unsewered, grazing, and undeveloped.
Land cover and land uses within a 5-kilometer radius of the upstream watershed of each sampling station will be analyzed as per the Stream Pollution Trends Monitoring (SPoT) program under California’s Surface Water Ambient Monitoring Program (SWAMP). This method allows for the assessment of the land cover and land uses that are most likely to influence the samples that were collected at each sampling station. This method will assist Regional Board permitting staff and county and local water quality management agencies to address the sources most likely contributing to fecal pollution. If pollution persists in these locations, further assessment of a greater upstream radius may be conducted for those sites that need more information.

Additional Studies

Jolly Giant Creek Monitoring Study

Jolly Giant Creek is currently on the Section 303(d) list as impaired for REC-1 beneficial use. After evaluating MST data collected from Jolly Giant Creek during the Impaired Streams Monitoring Study, Regional Board Staff noted a high occurrence of human-specific MST markers in all samples collected from the sampling station in Jolly Giant Creek (Jolly Giant Creek at Samoa Boulevard). In response, Regional Water Board Staff, along with the staff members from the Environmental Services Department of the City of Arcata, and the Humboldt Baykeeper non-profit, developed a monitoring plan to collect additional wet and dry weather samples to determine the current status of fecal pollution in Jolly Giant Creek, identify the potential source(s) of pollution, and inform development of pollution control strategies if needed. Fecal indicator bacteria (E. coli, and enterococci), and microbial source tracking (dog-, gull-, human-, and ruminant-specific markers) data were collected from five sampling stations along Jolly Giant Creek. Sampling sites were selected along Jolly Giant Creek at locations where it is above ground and near potential human fecal pollution sources (leaking sewage pipes, illegal sewage dumping and/or unhoused population inputs). Fecal indicator bacteria data were evaluated to assess exceedances of the statewide REC-1 water quality objective, and microbial source tracking data were evaluated to determine the potential sources of fecal pollution. Samples were collected from the locations listed in the table below.

The locations from where samples were collected for the Jolly Giant Creek Monitoring Study are shown in the figure below.

A map showing the locations from where samples were collected for the Jolly Giant Creek Monitoring Study

Reference Streams Monitoring Study

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

In conjunction with Impaired Streams Monitoring Study, 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 assess bacteria levels from sixteen (16) reference stream catchments, which are listed in the table below.

Humboldt County Department of Environmental Health (DEH) Advanced Protection Management Program (APMP) Surface Water Monitoring Study (Humboldt County APMP Study)

In addition to the data collected under the Source Assessment Study of the Coastal Pathogen Project MST data collected by Humboldt County under the Humboldt County Department of Environmental Health (DEH) Advanced Protection Management Program (APMP) Surface Water Monitoring Study (Humboldt County APMP Study) is also being analyzed to determine potential sources of fecal discharge. This study was developed by Humboldt County DEH in response to the requirement set forth by the OWTS Policy Section 9.3.2. Part of this section requires Local Agency Management Program (LAMP) local agencies to assess the extent to which groundwater and local surface water quality may be adversely impacted by OWTS as a component of their water quality assessment program. To accomplish this task Humboldt County DEH have focused their assessment efforts on the surface waters within their APMP – the watersheds upstream of 303(d) impaired beaches – with ongoing FIB and MST sampling. Ongoing sampling efforts will help Humboldt County DEH determine where in these watersheds contamination is originating and better evaluate the extent of OWTS impact to water quality impairment. Further details about the Humboldt County LAMP can be found on the Humboldt County DEH Land Use Program Webpage.

Under the Humboldt County APMP Study, samples are being collected from eight (8) coastal streams within the APMP boundary. Samples collected between April 2019 and November 2022 were available at the time of analysis, and MST (dog-, gull-, human-, and ruminant-specific markers) data collected during this time frame have been included in the source assessment analysis described above. Sampling was conducted after the first rain of the year, and during the wet weather season. The sampling locations are listed in the table below.

The locations from where samples were collected for the Humboldt County APMP Study are shown in the figure below.

A map showing the locations from where samples were collected for the Humboldt County APMP Study

Project Documents, Milestones, and Timeline

The Coastal Pathogen Project is intended to result in recommendations for assessment and control of fecal waste sources in the coastal streams and ocean beaches listed as impaired for pathogens.  The results of the scientific work conducted under the Coastal Pathogen Project will be posted on this webpage following successful completion.