The Lake Champlain Basin supports a diverse array of natural plant communities and many rare plant species. Cobble shores, sand beaches and dunes, low-gradient rivers, emergent marshes, bogs and fens, floodplain forests, maple-ash swamps, hardwood-cedar swamps, pine-oak-heath sandplain forests, oak-hickory forests, calcareous cliffs, alpine tundra, and cedar-pine lake bluffs are some important natural communities found in the watershed. The mineral-rich bedrock and soils of this region support natural communities high in plant diversity, including several plant species rarely encountered outside the region.
In the Vermont portion of the Basin, 56 plant species are listed as endangered or threatened under Vermont law. New York State published a list of protected native plants that includes endangered, threatened, vulnerable and rare species. One hundred and twenty species on this list are associated with Lake Champlain and its wetlands, tributaries, shorelines, and bluffs. Common threats to these rare plants and plant communities are land development and invasive species.