Produced for the North Carolina Coastal Nonpoint Source Program
by the North Carolina National Estuarine Research Reserve
Addressing Microbial Pollution
in Coastal Waters
North Carolina’s coastal areas are valued a b
for their economic, ecological, and cultural
significance. Our coastal counties rely on both
fishing and tourism for their economic health. For
example, in 1999, visits to local beaches accounted
for approximately 24% of total state tourism, with
11 million visitors to the North Carolina coast1 .
These visitors and residents expect clean waters
for commercial fishing, recreational fishing, boating
and swimming. Anything that indicates that water
is polluted has a detrimental affect on local Figure 1. These signs denote (a) waters closed to shell-
economies. fish harvesting and (b) recreational swimming adviso-
In many places along the coast, visitors see ries, due to elevated levels of indicator bacteria.
signs prohibiting shellfish harvesting (Figure 1a).
Data from the National Shellfish Registry shows Microbes & Water Quality
that 364,000 acres of shellfish beds in North
Carolina have been closed since 1995 due to Microbes are defined as any microscopic
elevated levels of indicator bacteria2. Beaches have organism including protozoa (single celled organisms),
also been posted with swimming advisories (Figure bacteria and viruses. Most microbes are beneficial or
1b), which warn swimmers of possible health risks harmless to human health but some are pathogenic,
due to fecal contamination. Seventy-two percent of causing a variety of human diseases. Pathogenic
swimming advisories in North Carolina in 2001 microbes that are found in the aquatic environment
were due to elevated levels of indicator bacteria1. come from the feces of warm-blooded animals (birds
and mammals) that are deposited or wash into water.
Microbes are distributed to surface waters by
two types of pollution, point and nonpoint sources. Point
sources are defined by the U.S. Environmental
Protection Agency (EPA) as “any discernible, confined,
and discrete conveyance, including any pipe, ditch,
channel, tunnel, conduit, well, discrete fixture, container,
rolling stock, concentrated animal feeding operation,
landfill leachate collection system, vessel, or other
floating craft from which pollutants may be discharged.”
Nonpoint sources, as the term indicates, are diffuse
and caused by rainfall (i.e. stormwater), snowmelt or
irrigation flowing above and below ground. Both point
and nonpoint sources may contain microbes, which
may then be deposited into freshwater bodies,
wetlands, coastal waters, and drinking water. Human
sources of microbial contamination are more closely
Figure 2. Three major source groups of fecal associated with point source pollution. Non-human
contamination in coastal waters sources are more closely associated with nonpoint
State Agencies and Microbial Pollution
B eing aware of the state
Table 1. Microbial Related Responsibility and State Agency
agencies and their water quality
related responsibilities can be a Activity Agency
considerable help to local Microbial water quality monitoring
governments as they address DWQ - Environmental Sciences Branch
for fresh and estuarine waters
microbial contamination of waters in DEH - Shellfish Sanitation &
Microbial water quality monitoring
their jurisdictions. The two primary for estuarine and ocean waters Recreational Water Quality Section
state agencies that have
Shoreline Surveys of shellfish DEH -Shellfish Sanitation &
responsibilities related to the growing areas Recreational Water Quality Section
management of microbes in coastal
Regulating shellfish harvesting DMF
waters from nonpoint sources of
pollution are the Division of Water Recommending and tracking DEH - Shellfish Sanitation &
shellfish growing area closings Recreational Water Quality Section
Quality (DWQ) and the Division of
Environmental Health (DEH)– both Assessing loss of use of
within the Department of Environment swimming waters and DWQ - Planning Branch
and Natural Resources. Table 1
identifies the major responsibilities of TMDL development DWQ - Planning Branch
these two agencies, as well as the DEH - Shellfish Sanitation &
Posting swimming advisories
Division of Marine Fisheries (DMF), Recreational Water Quality Section
which regulates shellfish harvesting.
Currently, state agencies use “indicator” organisms to identify
waters that might have significant concentrations of harmful
microbes. The preferred U.S. Food and Drug Administration’s
indicator for shellfish waters is the fecal coliform group (Figure 3)
and the U.S. EPA approves of using Enterococcus as an indicator
for recreational bathing waters3. These bacteria groups, which are
relatively easy to identify and quantify, are found in most warm-
blooded animals and are extremely abundant in feces. While usually
Figure 3. Escherichia coli (E. coli) , a not pathogenic, their presence in a water sample in significant
common rod-type fecal coliform bacterium. numbers indicates that pathogens may also be present. However,
Source: Shirley Owens and Michigan State the “indicator” does not reveal the source of the microbial pollution.
Microbial Source Tracking Techniques
Determining the source of microbial pollution (e.g. feces of animals or human septic/sewage systems)
is difficult, but is an important aspect of water quality management (Figure 2). A general term for this new
and developing field of research is “Source Tracking”.
There are many highly technical source tracking methods being developed, with two broad groups
that consist of microbial-based methods, called Microbial Source Tracking (MST), and chemical-based
methods, or Chemical Source Tracking (CST). These methods are still relatively new procedures being
tested in the scientific community to improve identification and quantification of individual pathogens and
are not necessarily feasible for local communities to conduct at this time.
While these technical microbial and chemical source tracking methods may eventually become
commonplace in water quality management, there are inexpensive approaches that communities can employ
now to help identify the sources of microbial contamination. A shoreline survey is one of these approaches.
North Carolina Shellfish Sanitation Section conducts shoreline surveys within the twenty coastal counties
every three years. The data are available for public use.
Conducting a Shoreline Survey
Communities may benefit from conducting their own shoreline surveys by improving their
understanding of: the land area that contributes pollutants to local waters, the sources of microbial pollution,
and the types of development with their jurisdiction. These benefits may help with other community projects
such as watershed or land use plans. A shoreline survey can take on many forms, from driving through the
survey area to a more complete door-to-door survey. Please keep in mind that a door-to-door survey involves
inspecting private property and thus there are legal implications associated with trespassing. Instead of
trespassing, simply walk or drive through the survey area to gain an understanding of the land uses within
the watershed. Regardless of the survey type, referring to the following guidelines and tailoring them to the
preferred survey style will gather the desired information:
• Notify local authorities that you are conducting a survey (including the county health department,
Division of Coastal Management and Shellfish Sanitation Section).
• Determine the boundary of the survey area.
• Estimate the population of the survey area.
• Drive-through the survey area to get an understanding of the possible pollution sources (i.e.
percentage of impervious surfaces, number and concentration of marinas, wastewater treatment
plants, agriculture, domestic pets, etc.).
• Expand your inspection by going door-to-door, pay attention to septic systems, stormwater drains
and ditches and canals.
Preventing & Reducing Microbial Contamination
One of the overriding issues associated with the delivery of
microbes to surface waters is nonpoint source pollution, and more
specifically, stormwater runoff (Figure 4). An analysis of 34 recent
urban stormwater monitoring studies conducted by the Center for
Watershed Protection has shown that most stormwater runoff samples
exceed bacteria water quality standards by a factor of 75 to 1004. It is
evident then, that to prevent microbial contamination, communities
must prevent stormwater runoff and improve the quality of the runoff
that does occur. Figure 4. Stormwater outfalls, like this
Land Use Planning one on a NC beach that empties onto
Increased stormwater runoff is one of the most evident products the beach, are noted during a shoreline
of human alteration of the landscape – which in turn has great impact survey.
on our water quality. Improved land use planning and management practices to reduce the volume of runoff
can be applied whether planning development for a region, a site, or an individual lot.
Developing with Water Quality Protection in Mind
Development that seeks to protect water quality must adhere to the following principles: maintain
site hydrology; minimize impervious surface area (thereby reducing stormwater runoff); and provide as
many opportunities as possible to treat and manage stormwater on site. The overall strategy of the design
process should include: finding ways to reduce stormwater runoff; keeping the water on site as long as
possible: reinfiltrating stormwater; and treating unavoidable runoff prior to release into nearby surface waters.
There is an increasing amount of data that indicates water quality is related to the percentage of
impervious coverage in the watershed. Impervious coverage may also be an indicator of microbial
contamination. Dr. Michael Mallin, a researcher at UNC-Wilmington’s Center for Marine Science, has
determined through studies on tidal creeks in New Hanover County, North Carolina, that the abundance of
fecal coliform bacteria is strongly associated with the percentage of developed land and more specifically
impervious surface coverage within the watershed. Impervious surfaces, consisting of roofs, roads, driveways,
sidewalks and parking lots, prevent infiltration of water into the soil and create a stormwater “superhighway”
that concentrates and carries pollutants quickly to downstream surface waters.
Stormwater Best Management Practices (BMPs)
Stormwater BMPs are another measure Table 24. Median Stormwater Fecal Coliform Bacteria
communities can take to reduce microbial loads Removal for Selected BMPs; n = number of studies
to coastal waters. Available data on the
Mean Stormwater Bacteria
effectiveness of various BMPs to reduce BMP
Removal Rate (%)
microbial loading is sparse4. However, data that
Ponds (excludes dry
do exist for control BMPs, including wet ponds, 70 (n=44)
extended detention pond)
stormwater wetlands, sand filters, vegetated
Wetlands 78 (n=39)
buffers and grassy swales, show that these
practices have a modest potential to reduce Filters (excludes vertical sand
filters and vegetated filter strips) 37 (n=19)
microbial levels, but are unable to reduce them
far enough to meet water quality standards in Swales (includes biofilters,
wet swales and dry swale) -25 (n=9)
most urban areas (Table 2) . They should be used
in conjunction with sustainable design, Ditches 5 (n=11)
watershed management plans, stormwater
management plans and public education campaigns.
Public Education and Outreach
Despite incorporating sustainable design techniques and
stormwater control BMPs, microbial pollution reduction goals will not
be achieved if the public is not educated on the importance water quality
and their role in water quality protection. An informed and knowledgeable
community results in greater support for community watershed planning.
Also, as the public becomes aware of the impact of their actions,
behavioral changes are more likely to result. Among the greatest need
for public education to reduce microbial pollution is the impact of Figure 5. Educating your constituents
stormwater runoff on water quality, sources of microbial pollution, septic about proper disposal of pet waste will
system maintenance, and proper pet waste disposal (Figure 5). help reduce microbial pollution.
North Carolina Department of Commerce: http://www.nccommerce.com
Potts, J.D. Personal Communication. 2003. Environmental Health Program Specialist, Shellfish Sanitation &
Recreational Water Quality Section, Division of Environmental Health, NC Department of Environment & Natural
U.S. Environmental Protection Agency, Chapter 17: Bacteria—Indicators of Potential Pathogens:
Center for Watershed Protection, 1999. Microbes and Urban Watersheds: II. Concentrations, Sources and
Pathways. Watershed Protection Techniques. Vol. 3, No.1, pp.549-620.
This document was produced with funds provided by the National Oceanic A reference document for
and Atmospheric Administration through the North Carolina Department of local governments on Microbial
Natural Resources, Divisions of Coastal Management and Water Quality, jointly Pollution is available through:
administered Coastal Nonpoint Source Program (Award #NA170Z1132). NCNERR Education Office
135 Duke Marine Lab Road
Beaufort, NC 28516