Human Health

Boy playing in stream

A number of contaminants can affect human health and the Lake Champlain ecosystem. People can be exposed to toxic chemicals while swimming, drinking water, or eating certain fish. Pathogens infect people when ingested, causing illness or disease. These substances enter the Lake in runoff and from wastewater treatment facilities. Some have been a long-time concern, and cleanup actions were taken decades ago. Others have become an issue for scientists more recently.

Blue-Green Algae

Cyanobacteria, also known as blue-green algae, are a naturally occurring type of bacteria that play an important role in aquatic ecosystems. Under certain conditions, they can grow prolifically and form potentially toxic blooms. The two toxins produced by cyanobacteria that are of most concern in Lake Champlain are anatoxin and microsystin. These toxins can cause skin irritation and gastro-intestinal illness, and can affect the liver, digestive system, and nervous system. Blooms may appear like thick pea soup or green paint. They form when warm surface waters combine with abundant phosphorus and calm winds that do not mix the lake water. Blooms usually occur in the summer months, and are more common in certain parts of the Lake, such as Missisquoi Bay, St. Albans Bay, and the South Lake. Blue-green algae blooms are one of the primary causes of beach closures on Lake Champlain.
Visit the Beach Closure map


Pathogens are disease-causing bacteria, viruses, and parasites that are present in human and animal waste. During rain events, runoff carries pathogens such as Escherichia coli (E. coli), giardia, cryptosporidiosis, and flatworms into streams and rivers and eventually Lake Champlain. Agricultural fields, faulty septic systems, and pet waste are common sources of pathogens. In urban areas dog droppings are one of the leading sources of E. coli. The greatest risk of pathogen exposure is in the days following large storms, when heavy rains cause combined sewer overflows (CSOs). During these events, sanitary sewer systems are overwhelmed by large volumes of water from storm sewers that enter through connected pipes. Public beaches along Lake Champlain were closed on more than 30 occasions between 2012 and 2014 as a result of elevated bacteria levels. For this reason, swimmers should use caution following heavy rain and stay informed about local conditions.


Toxic substances are chemicals that, at some concentrations, can harm plants and animals, including humans. These chemicals may affect the reproduction, growth, behavior, and survival of aquatic organisms. In general, they are found in low concentrations in Lake Champlain, but they can cause health-related problems, so are still a concern. Mercury and polychlorinated biphenyls (PCBs) are present at low levels throughout the Lake, and have been the target of past cleanup efforts. In 2000, the New York State Department of Environmental Conservation spent $35 million to dredge contaminated sediments from Cumberland Bay near Plattsburgh, NY. Toxic substances can come from a number of sources, including spills, hazardous waste sites, landfills, household hazardous materials, and atmospheric sources. Runoff from agricultural and developed lands can pick up motor oil, pesticides, metals, and de-icing chemicals. Some of these contaminants have accumulated in the tissues of several fish species, prompting Québec, Vermont, and New York to post fish consumption advisories. Recent studies have found that remediation efforts likely have had positive results with mercury concentrations decreasing significantly in some sport fish in recent years.

New Generation Contaminants

Scientists have recently documented pollutants in Lake Champlain that have not been identified before. A 2006 study by the U.S. Geological Survey found 70 different “new generation contaminants” present in low levels in Lake Champlain Basin waterways. These products include fire retardants, plasticizers, pesticides, fragrances, stimulants, medications, detergents, and anti-microbial additives associated with potential human health and ecosystem quality risks. The long-term effects of persistent, low-level exposure to substances on the ecosystem, aquatic life, and human health are not well understood. Monitoring and regulation of new generation contaminants is not consistent throughout the Basin’s three jurisdictions and is often minimally enforced at a local level. In 2012, the LCBP released a new Toxic Substance Management Strategy as a guide for resource managers in reducing toxic contamination. The strategy works under the premise of the precautionary principle: preventive measures are advised if any potential risk to ecosystem or human health exists, unless the substance is known to be harmless.