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Lake Champlain is among the largest natural lakes in the United States. Geologically and ecologically Lake Champlain is a sibling of the Great Lakes. About 18,000 years ago much of the northeastern and north central United States was covered by a thick blanket of ice which extended skyward at least far enough to cover Mt. Mansfield, Vermont's highest peak (1341 m above sea level). As the last glacial period came to an end, the glaciers retreated to the north leaving a large body of freshwater which included the Great Lakes, Lake Champlain, and much of the St. Lawrence River valley. As the glaciers continued to recede, sea water from the Atlantic Ocean flooded into the St. Lawrence valley and the Champlain valley creating the Champlain Sea (about 11,000 years ago). Over the next few thousand years, the land of the Champlain Valley, relieved of the burden of a thick layer of ice, gradually rebounded. As the water flowed northward into the St. Lawrence River, the sea water was replaced and diluted by freshwater from the surrounding basin.

For students and researchers of lake ecology, Lake Champlain is a terrific resource - truly a great lake. Lake Champlain supports biological communities similar to those found in the Great Lakes, but it has not experienced the same intensity of human settlement, impacts, or commercial utilization as its five larger "siblings". It therefore provides an excellent basis for comparison studies of large lake ecology.

Water quality in the lake and its tributaries is influenced by a combination of municipal, industrial, agricultural, and recreational uses throughout a relatively large area of two U.S. states and one Canadian province. The Lake Champlain Basin includes a small bit of southern Quebec, a large portion of upstate New York, and most of the state of Vermont. Water from the lake flows slowly northward into Canada's Richelieu River and empties into the St. Lawrence River. Environmental decisions regarding the lake and it's basin, therefore, must include interstate and international cooperation.

Lake Champlain is geologically subdivided into five distinctly different sub-basins, each of which represents a somewhat different set of limnological conditions. The South Lake (from the Poultney River north to Crown Point) is quite narrow, shallow, and turbid - much like a large, slow river. On the northern end of Lake Champlain lies Missisquoi Bay, a very shallow (< 4.5 m deep) and turbid part of the lake that receives water from both the state of Vermont and the Province of Quebec. Missisquoi Bay flows south into the Inland Sea, also known as the Northeast Arm. This rather large section of Lake Champlain lies to the east the Champlain Islands (South Hero, North Hero, and Isle LaMotte). Although fringed by some warm, shallow bays, much of the Inland Sea is fairly deep (over 30 m), cool, and relatively clear. South of the Inland Sea lies Malletts Bay - a rather small basin with restricted exchange with the rest of the lake due to a highway causeway on its north side (US Route 2) and a former railroad causeway on its west side. Over 80% of the volume of the entire lake is contained within the Main Lake, also known as the Broad Lake. This section runs from Crown Point north to Rouses Point, where the lake flows into the Richeleau River on its way to the St. Lawrence River and, eventually, the Atlantic Ocean. The Main Lake is quite deep, with much of it over 60 m and a few locations over 120 m in depth. Much of the Main Lake is clear and cold. The limnological diversity provided by these five sub-basins makes Lake Champlain all the more interesting and challenging for those interested in large lake ecology.