Water testing in Stonington's Wequetequock Cove has turned up human environmental DNA, according to a local coalition that has spent two years testing the cove. The group says dozens of tests have overwhelmingly confirmed human DNA in the water, with levels at times described as off the charts, while the town works to pinpoint exactly where it's coming from.
Paul Goetz, founder of the Wequetequock Clean Water Coalition, helped obtain testing in the cove and nearby tributaries and streams, as reported by WFSB. Goetz said two years and dozens of tests overwhelmingly confirmed human DNA in the water, with testing per Goetz confirming a human DNA ratio of 80 to 1. He believes failing septic systems are likely to blame for the contamination, and said testing detected both human DNA and E. coli DNA in the water, which he said points to human sewage.
The grassroots coalition formed last year to improve conditions in the cove, but the underlying problem is far from new. DNA testing in 2022 was able to narrow the source of pollution in the cove to human waste, according to CT Examiner, after DNA tests performed by Clean Up Sound and Harbors turned up high levels of human fecal coliform in surface runoff, the cove itself, and nearby wells.
Years of Red Flags Before the Recent Findings
Wequetequock Cove's water quality has declined for years, and algae blooms have been worsening, with cove wildlife also declining compared with the past. Save the Sound has consistently given the cove's water quality the lowest rating in the eastern part of the state, per the CT Examiner report, and the organization's Long Island Sound Report Card has handed the cove a D or F grade every year since 2018, according to Save the Sound.
One resident described a decline in water quality he had witnessed over the past 60 years, the same CT Examiner report noted. Separately, residents told Save the Sound that moon jellyfish hadn't been seen in the cove in three or four summers. Water-quality monitoring by Clean Up Sound and Harbors, underway since 2009, has identified unsafe levels of pathogenic bacteria in the cove, its pond, storm drains and ditches, and testing of private wells has found pathogenic bacteria present in 10 percent of wells in the area.
The organization's more recent sampling adds further detail: DNA source-tracking conducted in 2025 found evidence the contamination was human in origin, pointing to wastewater and potential septic-system sources. Testing in July found bacteria levels up to 12.5 times the state's single-sample maximum for swimming and 2.6 times the maximum for recreation, while bacteria in the cove's outflow to Little Narragansett Bay measured 23 percent above the shellfish-consumption threshold.
Town Points to Septic Systems, Weighs a Costly Fix
Stonington First Selectman Bill Middleton said the town is trying to pinpoint the contamination source and that officials continue testing water samples and narrowing down where it originates. Middleton said about 45 septic systems were in question as potential failures, and that property owners are responsible for them. He said septic failures don't just affect the property owner — they affect other people's health and water quality too, and that repairs will cost affected homeowners additional money.
Sewer service could fix the contamination problem, Middleton said, but it comes with a steep price tag: around $10 million. That figure matches the Water Pollution Control Authority's own estimate for extending sewers into the neighborhood, per the CT Examiner's reporting, which also noted the WPCA plans a sewer study to examine whether sewer lines could reach Wequetequock Cove. The WPCA is a five-member citizen body appointed by the Board of Selectmen that oversees the town's wastewater systems, and state law authorizes such authorities to acquire, construct and operate sewerage systems, according to the Town of Stonington.
Short of a full sewer build-out, the town has already landed funding for smaller-scale fixes. The Connecticut Department of Energy and Environmental Protection awarded a $545,000 grant for a stormwater and community-outreach project in the cove, with the town contributing $130,000, the Westerly Sun reported. The project is expected to include four bioretention systems, nine tree filters and 10 residential rain gardens, according to the Westerly Sun, part of a longer effort by residents and town officials to curb stormwater runoff into the cove.
Residents Say Regulators' Hands Are Tied
Ledge Light Health covers the affected area but has not identified any specific failing septic systems and cannot compel property owners to take action, limiting what regulators can do even as residents press for change. In response, Stonington is considering new ordinances that would require septic systems to be pumped every five years and inspected whenever a property changes ownership.
The Wequetequock Clean Water Coalition is separately pushing for mandatory well testing in the area. Resident Michelle Claffey had a shallow well when she moved to Stonington and drilled a new one after testing showed contamination, spending thousands of dollars in the process. She recalled that people in the area used to fish and crab off docks across the street — something that no longer happens.
Not every Connecticut shoreline mystery has ended with sewage as the culprit. In Branford's Short Beach neighborhood, recurring beach closures were ultimately traced to dog waste rather than a leaking septic system, according to CT Insider. Researchers there used microbial source tracking — DNA analysis similar to what's been applied in Wequetequock Cove — to trace contamination at Johnson's Beach, once ranked among the four worst beaches of 37 monitored by Save the Sound, finding that samples with the highest E. coli levels also carried the strongest canine bacteria markers, with stormwater runoff carrying the bacteria into the water.
For now, Stonington area residents are simply hoping for cleaner water next year, even as the town continues narrowing down the contamination's source and weighing whether a $10 million sewer expansion is the eventual answer.
