Paleolimnological data from three high-arctic ponds on Cape Herschel, Ellesmere Island, Canada, show that diatom assemblages were relatively stable over the last few millennia but then experienced unparalleled changes beginning in the 19th century. The environmental factors causing these assemblage shifts may be related to recent climatic warming. Regardless of the cause, the biota of these isolated and seemingly pristine ponds have changed dramatically in the recent past and any hopes of cataloging natural assemblages may already be fruitless.