In terms of litter, debris, waste water pollution (point sources) and toxic pollutants (excluding mercury) most of Lake Champlain has good water quality compared to other New England lakes. Occasionally there are localized pollution problems in particular bays, or at particular beaches. Otherwise, most waste water treatment plants have been upgraded, and the City of Burlington has separated the storm drains from its treatment plant, preventing overflows. The PCBs in Plattsburgh Bay have been dredged.
Mercury pollution is mostly airborne from the Midwest, so the mercury levels in Lake Champlain’s fish are probably as bad as, or worse than, other New England lakes. Mercury bio-accumulates in living organisms: the higher up on the food-chain, the more mercury is likely to be found in the organism. Thus relatively low levels of mercury contamination can lead to high levels of mercury found in living organisms. Because of its size, Lake Champlain can support larger fish species which often have longer life spans and are higher up on the food chain. Thus the large fish that Lake Champlain can support probably have higher mercury levels than smaller fish in smaller lakes. Note: this is a very general statement, since mercury levels also vary by species.
Phosphorus pollution, which exacerbates algae blooms, is the most serious problem in Lake Champlain—perhaps worse than in many New England lakes. Some of the reasons include: the Lake has a large ratio of watershed area to lake volume; the Lake Champlain watershed has a long and continuing agricultural history; the growing amount of paved and roofed surfaces due to development has increased phosphorus from storm water runoff; the historic and continuing use of the area for get-away camps which have poor or non-existent septic systems also contributes phosphorus to the lake; and some municipalities add phosphorus compounds to their water supply to reduce pipe corrosion. Phosphorus loading in Lake Champlain has led to a noticeable increase in algae growth in the past 30 years, and in blooms of toxic cyanobacteria (blue-green algae) in the past 10 years.
http://www.lcbp.org/bgalgae.htm
Lake Champlain Questions 