Following the Water: What New Research Is Telling Us About Fecal Pollution in the New River
Coastal Carolina Riverwatch’s latest Pure Farms, Pure Waters assessment combines
water sampling, microbial source tracking, aerial surveillance, on-the-ground investigations,
community engagement, and farmer outreach to better understand where fecal pollution is entering
the New River watershed—and what can be done about it.
A watershed connecting farms, communities, and fisheries
The Pure Farms, Pure Waters (PFPW) program is a series of collaborative efforts
led by Coastal Carolina Riverwatch (CCRW) to address water-quality concerns in the
White Oak River Basin. The work grew from conversations with commercial and
recreational fishers, researchers, community members, and coastal advocates who were concerned
about declining water quality and the effects that land-based pollution can have on downstream
fisheries and marine ecosystems.
The White Oak River Basin encompasses portions of Onslow, Jones, and Carteret counties and
includes the White Oak, New, Newport, and North rivers, along with smaller streams, wetlands,
estuaries, and coastal habitats. The basin supports commercial and recreational fisheries,
boating, wildlife, local agriculture, tourism, and communities whose quality of life is closely
tied to clean water.
How much fecal contamination is present in priority New River waters, and what can DNA source
tracking tell us about whether that contamination is associated with humans, hogs, poultry, or
multiple sources?
The project was supported by Waterkeeper Alliance and conducted with critical
research support from the University of North Carolina Institute of Marine Sciences
(UNC IMS), including Dr. Rachel Noble and her laboratory team. CCRW also partnered with
SouthWings for aerial monitoring of agricultural operations and other potential
pollution sources.
2025–2026 at a glance
How we studied the New River
Beginning in 2023, CCRW and UNC IMS developed a collaborative research effort to assess water
quality in areas potentially influenced by concentrated animal feeding operations, commonly
called CAFOs. The 2025–2026 phase continued that work with a stronger emphasis on
microbial source tracking.
Six sampling locations were selected to represent different portions of the New River watershed,
including small freshwater streams in the upper watershed, larger headwater streams, and a
higher-salinity site where freshwater enters the tidally influenced New River estuary.
Sites NR1 through NR5 were selected in part because of their proximity to a hog CAFO sprayfield.
All six locations provided public access to the water.
| Site | Landmark | Waterbody | Coordinates |
|---|---|---|---|
| NR1 | Beulaville Highway | New River | 34.919, -77.617 |
| NR2 | AI Taylor Road | New River | 34.967, -77.635 |
| NR3 | Petersburg Road | Squires Run | 34.928, -77.543 |
| NR4 | NW Bridge Road | New River | 34.849, -77.519 |
| NR5 | Rhodestown Road | New River | 34.843, -77.503 |
| NR6 | Onslow Waterfront Park | New River | 34.752, -77.433 |
What we measured
During each monthly sampling event, CCRW collected field measurements for
pH, temperature, dissolved oxygen, salinity, and conductivity using a YSI
multiparameter instrument. Water samples were transported on ice to UNC IMS and processed
promptly to preserve sample integrity.
Laboratory work included fecal indicator bacteria testing for E. coli,
Enterococcus, and total coliform bacteria. Samples were also filtered and preserved for
microbial source tracking analysis using molecular markers associated with
human, swine, and poultry fecal sources.
Digital PCR, or dPCR, allowed the UNC IMS team to detect and quantify host-associated gene
markers. This provides information that conventional bacteria testing alone cannot: not simply
whether fecal contamination is present, but evidence about the types of sources contributing to
that contamination.
Drought was an important part of the story
CCRW had planned supplemental sampling after significant rainfall to investigate how runoff
changes bacterial and pollutant loading. Severe drought conditions during the 2025–2026
sampling window meant those rain events did not occur, so supplemental post-rain samples
could not be collected.
Average fecal indicator bacteria concentrations were lower than those measured during the
2023–2024 PFPW study. The report identifies the large difference in rainfall between the two
study periods as a likely contributor. The earlier sampling period included several rain
events; the 2025–2026 period included none of the significant rain events needed for
targeted post-rain sampling.
That makes one result particularly important: substantial bacterial contamination
was still documented during dry conditions.
Finding #1: Fecal indicator bacteria remained widespread
37 of the 48 water samples—77%—had E. coli and/or Enterococcus concentrations
above the EPA recreational water-quality values used by the project for comparison.
Site NR3 at Petersburg Road/Squires Run consistently showed elevated
concentrations of both E. coli and Enterococcus compared with the other monitored sites.
E. coli and Enterococcus are fecal indicator bacteria. Their presence at elevated concentrations
signals fecal contamination and can indicate conditions in which disease-causing microorganisms
may also be present.
For context, the report used an Enterococcus single-sample recreational value of
104 MPN/100 mL and the EPA historical single-sample E. coli criterion of
235 MPN/100 mL as comparison points.
classified as recreational waters. The EPA recreational criteria were used as a consistent
benchmark to help interpret the magnitude of bacterial contamination, not as a regulatory
classification of the sampled sites.
Finding #2: DNA source tracking points to multiple fecal sources
Bacteria measurements tell us fecal contamination is present. Microbial source tracking helps
move the investigation one step further by searching for DNA markers associated with specific
host sources.
Human-associated marker
The human-associated HF183 marker was detected across all six sampling
locations and was the most consistently detected of the molecular markers evaluated.
Swine-associated marker
The swine-associated Pig2Bac marker was also detected across all six
sampling locations. Detection was less frequent than HF183, but the analysis documented
occasional higher-concentration events, particularly at NR1.
Poultry-associated marker
Poultry-associated DNA markers were detected less frequently and were primarily observed
at NR2 and NR3.
Multiple pollution pathways
Statistical analysis found only weak, non-significant relationships among the three
molecular markers, suggesting that sources may enter the watershed independently or during
different episodic contamination events.
What the DNA results do—and do not—tell us
The molecular data document the presence of human-, swine-, and poultry-associated fecal
markers in the New River study area. They do not yet establish the relative share of
pollution attributable to each source.
Concentrations of molecular markers can vary substantially in raw waste. Additional research,
including characterization of markers in relevant source material, is needed to strengthen
source attribution and determine the relative importance of human wastewater, hog waste, and
poultry waste across the watershed.
CCRW’s collaboration with UNC IMS provides an important foundation for continuing that work.
Finding #3: Most basic water-quality parameters were relatively stable
Temperature, dissolved oxygen, pH, conductivity, salinity, and related field measurements were
compared with the earlier 2023–2024 sampling period using site-level averages.
Most parameters showed minimal change between the two study periods. The clearest difference
was salinity at the downstream, tidally influenced NR6 site. That difference
was statistically significant.
The report notes that the change may reflect stronger estuarine influence associated with the
2025–2026 drought, although tides and the timing of individual sampling events may also have
contributed.
Why this matters downstream
The New River begins and ends within Onslow County before reaching coastal waters that support
fishing, recreation, aquaculture, wildlife, and other water-dependent uses. That geography gives
researchers an important opportunity to examine how pollution generated on the landscape moves
through tributaries and downstream toward the estuary.
Nutrients, fecal bacteria, and other contaminants from improperly managed animal waste,
wastewater, stormwater, and other sources can move through ditches, streams, and drainage
networks. Understanding those pathways is essential for identifying appropriate solutions.
Looking beyond the sampling bottle: aerial investigations
Water sampling was only one part of Pure Farms, Pure Waters. Through a partnership with
SouthWings, CCRW conducted routine aerial investigations over Onslow County
to observe changing land uses and identify conditions that warranted additional investigation
or regulatory review.
Flight plans included monitoring of hog operations, new poultry facilities, uncovered poultry
litter, potential harmful algal blooms, municipal infrastructure, wastewater facilities,
development, major tree clearing, and other activities with the potential to affect nearby
waters.
GPS-tagged photographs and written observations were used to document areas of concern.
Ten monthly reports were submitted to the North Carolina Department of
Environmental Quality during the reporting period, with information also shared with
Waterkeeper Alliance. Quarterly reports compiled observations relating to both hog and poultry
operations to support regulatory review and follow-up.
In several instances, repeated flights documented concerns at the same locations over time.
Continued monitoring is important because aerial observations can identify conditions that are
difficult to see from a public roadway or from the water.
From the air to the water: site investigations
Quarterly and as-needed field investigations complemented the aerial work. Kayak, wading, and
shoreline assessments allowed the team to examine drainage pathways and potential pollution
sources that may be hidden by vegetation, infrastructure, or distance from public roads.
During a December 17, 2025 kayak investigation near NR4 and NR5, CCRW documented
stormwater pipes and outfalls, discarded fishing line, large plastic and Styrofoam debris,
an orange bacterial mat, deteriorating structures, and areas with limited shoreline buffers.
Observations, photographs, and GPS points were recorded in Survey123 and reviewed in ArcGIS,
allowing field observations to be mapped alongside water-quality sampling locations and other
watershed information.
Research that reaches beyond the laboratory
PFPW was designed not only to collect data, but also to make water-quality science accessible
and useful to the people who live, farm, fish, and work throughout coastal North Carolina.
Throughout the project, CCRW used newsletters, social media, educational videos, website
updates, community events, farmer visits, surveys, and an ArcGIS StoryMap to explain how
agricultural pollution, wastewater, stormwater, and other land-based sources can influence
downstream waters.
Water Quality for Fisheries Symposium
The 2025 Water Quality for Fisheries Symposium brought together more than
100 fishermen, farmers, researchers, students, agency representatives, and community
advocates at the Duke University Marine Lab. PFPW intern Jocelyn Perry presented
project research during the symposium poster session, helping connect technical monitoring with
community discussion.
Community events
PFPW outreach was carried into farmers markets, environmental celebrations, and community
gatherings across the region. Highlights included Oysterpalooza in Surf City, Sturgeon City
Earth Day in Jacksonville, Ocean Fest in Surf City, the Olde Beaufort Farmers’ Market, and the
Onslow County Farmers’ Market.
These events created opportunities not only to share information but to listen. Residents
identified pollution, flooding, and water-quality concerns, learned about nutrient pollution
through interactive activities, and participated in the PFPW community survey.
Supporting farms that are working to protect water quality
Pure Farms, Pure Waters also recognizes an important distinction: industrial animal
agriculture is not the same as the many small and independent farms that are working every day
to build resilient local food systems.
CCRW met directly with farmers to understand their environmental stewardship practices,
business realities, challenges, and resource needs while helping increase the visibility of
locally operated farms.
Southern Sheep Company
During Shearing Day in Richlands, CCRW engaged more than 60 attendees, shared educational
materials, gathered public survey responses, and talked with community members about
barriers to buying locally.
Ocean Natural Farm
The Newport farm, operated by Michael Murdoch and Deede Miller, is Certified Naturally
Grown and uses 100% off-grid solar energy. Conversations focused on environmental
conditions, market access, operational constraints, and community support for local
producers.
Shenk Family Farm
Rachel and Joe Shenk operate an open-pasture and forest-based livestock farm using
rotational grazing. The visit highlighted both the value of diversified local food systems
and the resource challenges facing independent producers.
GiGi’s Farm
Helen and Joe Gross operate a flower, herb, and berry microfarm in Swansboro. Practices
highlighted during the visit included no chemical soil additives, no-till methods,
companion planting, water conservation, pollinator habitat, and hand pest management.
What community members told us about local food
CCRW received 39 public survey responses. Although the survey was not designed
to represent every resident of the basin, the responses provide useful insight into community
interest, purchasing behavior, and barriers to supporting local farms.
The results reveal a gap between interest and behavior. People strongly value
local food, but practical barriers can prevent them from purchasing it as often as they would
like.
Frequently reported barriers included travel distance and convenience, price, lack of knowledge
about where to purchase local products, uncertain availability, and limited selection.
Respondents said better availability, stronger relationships with farmers, support for the local
economy, reduced environmental impacts, and better pricing could encourage them to purchase
locally more often.
Environmental stewardship also mattered. Respondents identified reducing chemical use,
responsible animal-waste management, cover crops and buffers, and wetland protection as
important farming practices. 87.2% gave an affirmative response indicating confidence
that food choices can help protect waterways and ecosystems, while the remaining
respondents were neutral or not confident.
What farmers told us
Four farmers responded to the producer survey. Because of the small number of responses,
CCRW appropriately treats these findings as preliminary insight rather than
statistically representative results.
All respondents indicated that agricultural best management practices were very important to
their operations. Reported practices included soil testing, nutrient-management planning,
cover crops, vegetated buffers, conservation tillage, and livestock-waste management.
The most common barriers to additional conservation work were the
cost of equipment or infrastructure, limited financial support, and time and labor
constraints. Farmers expressed interest in on-farm consultation, additional financial
assistance, peer-learning opportunities, workshops, education, and better access to cost-share
opportunities.
not have to be competing goals. Farmers need programs that recognize operational realities,
make technical help easier to access, and provide sufficient financial support for conservation
practices.
Making the science easier to explore
CCRW staff and interns also developed a Pure Farms, Pure Waters ArcGIS StoryMap to translate
the project into a more visual and accessible format. Interactive maps help readers understand
the geography of the watershed, the locations of monitoring sites, and the relationship between
upstream land use and downstream waters.
The StoryMap, detailed research findings, project updates, and the complete final report are
available through the Pure Farms, Pure Waters project page.
Where the work goes next
The 2025–2026 results give CCRW and its partners a stronger foundation for continued research,
public education, policy work, and watershed protection—but they also identify important
questions that remain unresolved.
Continue microbial source tracking
Additional laboratory work can help determine the relative importance of human wastewater,
swine waste, poultry waste, and other fecal sources. Characterizing marker concentrations in
source material will strengthen interpretation of the DNA data and help identify where future
investigations should be concentrated.
Study runoff when the rain returns
Because severe drought prevented post-rain sampling during this project period, future
monitoring after significant rainfall is particularly important. Wet-weather sampling can help
determine how bacteria and animal waste move from the landscape into streams during runoff
events.
Strengthen accountability and enforcement
CCRW will continue using monitoring data, aerial observations, field investigations, and
partnerships to support stronger enforcement of existing animal-waste protections and to
communicate documented concerns to state decision makers.
The final report identifies several policy and legal pathways for continued evaluation,
including Clean Water Act tools, the Resource Conservation and Recovery Act, North Carolina’s
Right to Hunt and Fish Amendment, possible 60-day notice strategies, and efforts related to
development of Total Maximum Daily Loads where the science and law support those approaches.
Support local farmers
CCRW can use the survey findings to help close the gap between consumers who want to buy local
and farmers who need stronger market access, technical assistance, and financial resources.
Partnerships with Soil and Water Conservation Districts, Cooperative Extension, and the
Natural Resources Conservation Service can help connect producers with conservation planning,
cost-share programs, technical assistance, and grant opportunities.
Turn research into better policy
Monitoring is most valuable when it leads to action. By combining peer-supported scientific
research, community knowledge, farmer perspectives, field observations, and policy analysis,
CCRW will continue working toward solutions that protect water quality while supporting the
communities and local economies that depend on the White Oak River Basin.
A collaborative effort
Pure Farms, Pure Waters was made possible through support from
Waterkeeper Alliance and collaboration with the
University of North Carolina Institute of Marine Sciences and
SouthWings.
2025–2026 report and project contributors
Dr. Rachel Noble, UNC Institute of Marine Sciences
Emma Dempsey, PhD Candidate, UNC Institute of Marine Sciences
Zoe Schubert, Laboratory Technician, UNC Institute of Marine Sciences
Lisa Rider, Executive Director, Coastal Carolina Riverwatch
Riley Lewis, Former White Oak Waterkeeper, Coastal Carolina Riverwatch
Christina Boxberger, White Oak Waterkeeper, Coastal Carolina Riverwatch
Jocelyn Perry, PFPW Intern, Coastal Carolina Riverwatch
Saisha Neilsen, PFPW Intern, Coastal Carolina Riverwatch
Rolf Wallin, Volunteer Pilot, SouthWings
We are also grateful to the farmers, fishers, volunteers, community members, agency staff,
researchers, partner organizations, and supporters who shared their time, experience, and
knowledge throughout this work.
Read the full assessment
The complete Pure Farms, Pure Waters 2025–2026 Final Report provides the
detailed research methodology, bacteria and DNA analyses, maps, figures, survey findings,
outreach activities, advocacy work, references, and recommendations behind this summary.
Visit the project page to read the full report and follow Coastal Carolina Riverwatch’s
continuing work to protect the New River and the greater White Oak River Basin.
Pure Farms, Pure Waters: Full Report & Project Page
Coastal Carolina Riverwatch works to protect the quality of water and quality of life throughout
North Carolina’s White Oak River Basin.