Phosphorus is a nutrient that can limit plant growth. Too much phosphorus stimulates the growth of algae, which can turn water green and murky, cause foul odors, impair drinking water supplies, and deplete oxygen as the algae decay. Low oxygen levels can cause fish kills and deplete insect and microscopic organism populations that provide the all-important base of the lake's food chain. Other sources of phosphorus are more scattered, primarily run-off from farms and urban areas. The watersheds of Missisquoi Bay, Otter Creek, and the South Lake have been targeted as top priorities for phosphorus reduction.
Wetlands are some of the most threatened natural communities in the Lake Champlain Basin.
Roughly 35 percent of Vermont's wetlands have been lost since European settlement. The Vermont Department of Environmental Conservation estimates that from 1990 to 1993, between 200 and 400 wetland acres were lost each year. These losses were concentrated in the Lake Champlain Basin, and especially in rapid growth areas such as Chittenden County. This loss of wetlands was incremental, with hundreds of projects involving one acre or less of wetland alteration. Wetlands provide critical habitat for many kinds of fish, for mammals such as otters and mink, and for many species of reptiles and amphibians.