Bristol: DNA testing and pollution tracking in the Pemaquid River


Rachel Bizarro – Bristol Town Clerk

David Cheney – Bristol Shellfish Committee

short project summary (PDF)


The Town of Bristol, in partnership with the Bristol Shellfish Committee, the consulting agency FB Environmental Associates, and the Pemaquid Watershed Association, has been working to track pollution sources in the Pemaquid River and surrounding waterways.

Oyster conservation project, Damariscotta River, May 2021 (Photo by David Cheney)

DNA Testing

The Pemaquid River is listed as impaired by the Department of Environmental Protection due to elevated fecal indicators; shellfish harvesting is conditionally approved in the northern portion of the river and prohibited in the southern portion. The Bristol Shellfish Committee contracted with FB Environmental Associates, a Portland based consulting firm, for water quality testing in the Pemaquid River in 2019 and 2021, and in the Eastern Branch of the Johns River in 2021.  

During the summer of 2019, FB Environmental collected thirteen water quality samples during dry weather at known fecal contamination “hotspots.” Eight of the samples were sent to the University of New Hampshire for DNA analysis, which confirmed human contamination in one tributary and beaver and goose contamination in another. The testing alerted the Bristol Shellfish Committee to the environmental impact of small farms near the river, leading the committee to invite farm owners to hear FB Environmental’s final report at a presentation at a Shellfish Committee meeting.

In 2021, FB Environmental staff collected water samples from the East Branch of the Johns River, which crosses the town boundary into South Bristol.

The Eastern Branch is classified as “conditionally approved,” although a prohibited area below Foster Island is a favorite spot for clammers. The firm gathered water samples at seven sites, two of which showed low levels of human and Canadian goose DNA, and optical brighteners, which can indicate human fecal contamination. The sites that tested positive were located near a manmade trout pond and an area with sloping fields and no vegetation buffer.

Soft shell clams in the Johns River (Photo by David Cheney)

Additional sampling taken during wet weather near a small poultry farm tested positive for low concentrations of chicken fecal waste. FB Environmental contacted the landowner to discuss a site assessment, and the landowner applied for a nutrient management plan grant.

Oyster conservation project

Bristol’s 2019 conservation project for harvesters focused on water quality in the Pemaquid River. Shellfish Committee member Dave Cheney proposed collecting oysters from the Damariscotta River and broadcasting them into the Pemaquid River to see if the oysters would have a cleansing effect on water quality. The Damariscotta River has clean water and abundant oysters, both wild and farmed, and oyster shell mounds over 1,000 years old. The research of Bonnie Newsom, an Indigenous archeologist at the University of Maine, shows that Indigenous oyster fisheries were sustained for 5,000 years or more, and that this stewardship tradition has relevance for contemporary harvesting and management practices.

A group of volunteers collected more than 6,000 oysters along the banks of the Damariscotta River and transported them to a channel in the Pemaquid River where three streams converge. By the end of the season, the oysters had grown nearly two inches, and after three years of relaying oysters, a broodstock is growing and harvesters are starting to see wild oysters in some places. As coastal waters warm, David Cheney notes that oysters reproduce at higher temperatures than clams, and as for water filtration, “they work for free.”


  • The Shellfish Committee expanded their search to consider not just contamination from the natural environment but also the impact of local agriculture on the river
  • There was a need for more people power and volunteer support as well as more hands-on conservation projects for license holders, such as planting vegetation along the shoreline
  • This project struggled with low clammer participation in conservation projects
  • FB Environmental recommended further microbial source tracking (MST), looking into possible septic system malfunctions, improving shoreline buffers in certain places to capture pollutants and discourage geese from landing on the water  

The Bristol Shellfish Committee plans on working with FB Environmental to take more samples during different weather conditions at Schoolhouse Cove, the Eastern Branch of the Johns River, and Pemaquid Falls to continue tracking the source of the bacterial contamination.


  • 2017

    Maine DEP collects water samples from the freshwater tributaries of the Pemaquid River to identify sources of fecal contamination

  • 2018

    The Town of Bristol, the Shellfish Committee, FB Environmental Associates, and Pemaquid Watershed Association begin sampling in the Pemaquid River Watershed

  • 2019

    Conservation project transplanting oysters from the Damariscotta to the Pemaquid River begins

    Town of Bristol contracted with FB Environmental for DNA testing in the Pemaquid River

    (Photo by David Cheney)

  • 2021

    FB Environmental collected water samples in the Eastern Branch of the Johns River


Bristol Shellfish Conservation Committee

“Fall 2021 Pemaquid River Hotspot Sampling,” FB Environmental

“Eastern Branch Johns River Fecal Source Tracking,” FB Environmental

“Pemaquid River 2019 Monitoring Report,” FB Environmental

“Indigenous oyster fisheries persisted for millennia and should inform future management”

“UMaine researchers co-author Smithsonian study about Indigenous oyster consumption”