It is commonly assumed that High Arctic lakes and ponds were not affected by direct local human activities before the arrival of Europeans, because most native peoples were primarily nomadic, maintained relatively low population densities, and practiced unintrusive hunting and gathering technologies. Our archeological and paleolimnological data show that this was not always the case. Thule Inuit whalers, whose winter settlements consisted of houses constructed from the bones of bowhead whales on Somerset Island between about anno Domini 1200 and 1600, markedly changed pond water quality and ecology. The arrival of whalers 8 centuries ago caused marked changes in water chemistry and the expansion of moss substrates. Although whalers abandoned the area >4 centuries ago, the legacy of these human disturbances is still evident in the pond's present-day limnology and is characterized by elevated nutrient concentrations and atypical biota. This is the earliest reported paleolimnological record of changes in aquatic ecology associated with local human activities in Canada or the United States, or for any circumpolar ecosystem.