While leaky septic tanks continue to be an assumed key contributor to bacterial contamination of Lowcountry waterways, experts and investigators on Edisto Island are squinting with reptilian eyes at another possibility.
Dr. Amy E. Scaroni, a wetlands biogeochemist who helped develop the Edisto Island Watershed Plan, says research into bacteria levels in water has long been missing one crucial answer.
“The S.C. Department of Environmental Services does monthly monitoring that establishes the water levels and designated impairments, but that bacteria can be coming from anywhere,” she said. “When it comes to pinpointing the source — we’re still missing that smoking gun.”
At different impaired sites, she added, that bacteria can be coming from several different sources, with leaky septic tanks as a big contributor.
“Septic tanks, even working ones, can be sources of bacteria and nutrient pollution in our coastal waterways,” Andrew Wunderley, executive director of Charleston Waterkeeper, told the Charleston City Paper in December 2025. “When a septic system is improperly sited or installed, leaks or is flooded, microbial and nutrient pollution move into nearby waterways and marshes.”
But while talking to community members on Edisto Island, Scaroni said another big possible culprit came up in conversation again and again — alligators. And now, that speculation is driving the potential for future research endeavors.
The new suspect
The idea that alligators could be to blame for water contamination — even partially — is still new. Formal research hasn’t even started on whether the Lowcountry’s alligators have an effect on water quality. But the possibility is enough to intrigue several scientists working with water in and around Edisto and the ACE Basin. And if alligator poop is a water quality culprit in one place, its impact could be all over the Lowcountry.
Tom Austin, director of land conservation at the Edisto Island Open Land Trust, said recent efforts have been employing state-of-the-art microbial source tracking systems throughout the watershed to characterize bacteria pollution sources, matching them to an existing database. But data processing and research is still ongoing, and results have been inconclusive.
“My research partners and I have had quite a few discussions about the potential for alligators to be surreptitious contributors to the profile of fecal coliform bacteria being observed in the water column within the Edisto Island watershed,” he said. “It’s a variable we have yet to disentangle.”
A research paper published in 2010 by the Journal of Applied Microbiology indicated alligators may produce an exceptionally high concentration of bacteria in the water, but their biology makes it difficult to measure the impact. Why? Because alligators are cold-blooded carnivores, radically different from warm-blooded humans. The bacteria that live in their guts can have a hard time getting established in people, but the pollution still negatively impacts Lowcountry waters.
Alligators, in fact, have a heavily depressed metabolism compared to other animals in Lowcountry marshes, meaning they eat far less often and produce much less waste by volume. But the fact that alligators expel waste directly into the water makes measurement difficult. But when there are a lot of alligators in one area, the story could change.
“These facts imply that, when many alligators are concentrated in one location for an extended period of time in warm weather with ample food, they could become a driving contributor of fecal indicator bacteria into the water column for a brief window of time,” Austin said.
More than one cause
The research team in Edisto is using microbial source-tracking to compare bacteria samples against canine, bird and livestock waste, though Scaroni said she wants to add deer — and later, possibly alligators — to the database.
“It’s an expensive process, and it’s all locally dependent,” she said. “Dogs come up a lot, and maybe not so much here on Edisto, but in more urban areas or high-density developments. In one neighborhood, there could be 200 dogs, and that’s a much higher population density than you’d expect for any wild animal population.”
Austin said he thinks raccoons are a bigger contributor than a lot of people would think, “as evidenced by … the well-known propensity for raccoons to utilize docks to more easily access waterways — and their pension for establishing latrines on said docks.”
“That’s my gut thought (pun intended), but we’ll see what the research and science bears out.”
Urban developments also have a large impact on animal populations, pushing them to higher concentrations in smaller areas, leading to big bacteria spikes in that spot’s water column. But a healthy ecosystem, Scaroni said, is often capable of handling these increased levels of pollution. The bottom line, according to Austin, is that humans are a bigger threat to water quality than any animal.
“A human catching something from an animal is not particularly common,” he said. “However, as might be obvious, human waste contains pathogens for human diseases that are specifically adapted for infecting humans.”
That’s why even the trust is working to repair and replace failed septic tanks for low-income homeowners. “Failed septic systems are a clear pollution source above and beyond the natural baseline that we, as a rural unincorporated community, have a modicum of control over,” Austin said.
“But at the same time, we’re also investing in the research and partnerships necessary to get to the hard facts at the bottom of the issue.”
Lowcountry water pollution draws lots of attention
Charleston and its surrounding communities sit at the center of a unique estuarine ecosystem marked by tidal rivers, creeks and marshes. The waters are home to pelicans, dolphins, redfish, oysters, shrimp and more, and often appear at the top of international destinations.
But every month, analyses conducted by area scientists and experts reveal dangerous levels of bacteria in several bodies of war popularly used by fisherman, swimmers and boaters.
Though the primary source of the bacteria is still unclear, the main concerns since initial studies in 2002 have been septic tanks in disrepair, improperly discarded pet waste, stormwater runoff and wildlife. Renewed DNA testing started in the 2020s that corroborated reports from decades earlier. Weekly water quality tests by groups like Charleston Waterkeeper also remain consistent year over year, as highlighted in recent years by the Charleston City Paper.
In 2021, water samples from the Ashley and Cooper rivers, Shem Creek, James Island Creek and Charleston Harbor were analyzed by the College of Charleston. The samples contained DNA from pathogens like tuberculosis, staph, cholera and E. coli bacteria. While the presence of DNA from these pathogens doesn’t necessarily cause illness, experts say it raises concerns for swimmers and other recreational users, especially those who are immunocompromised.
The problem isn’t new.
“From the beginning, Charleston has struggled with sewage treatment and water pollution,” Charleston Waterkeeper Executive Director Andrew Wunderley wrote in a September 2024 blog post. “In the 1800s, the city faced dysentery and typhoid outbreaks from contaminated drinking water, and cases of hepatitis linked to oysters harvested from polluted waters.”
Construction of a sewage collection system began in 1894 on Broad Street in downtown Charleston. Over the next 40 years, it was extended to other parts of the peninsula. But even after its completion, raw sewage was still dumped into the harbor without treatment, a practice which remained legal until 1970.
Now, experts are raising alarms about septic tanks, which, despite reports that say they are a huge source of bacterial pollution, are continuing to be proposed for new developments on Johns Island and in Awendaw.
And bacteria-laced floodwaters, a natural occurrence that is difficult to mitigate with legislation and local ordinances, are becoming more and more common. According to Charleston Waterkeeper, models show that Charleston experienced about two flood days per year in 1950, compared to 25 days per year in 2014, with predictions of 60 days per year by 2051.
James Island has been working on the issue for years, with proposals to expand the existing sewer system to rural areas. Meanwhile, Mount Pleasant is focusing on providing affordable and accessible septic repair and replacements to mitigate their impact.
These initiatives and ordinances, local leaders hope, could become a model for neighboring municipalities that will together make a big difference in Lowcountry water quality.
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