Great Slave Lake, one of the world’s largest and North America’s deepest lake, has undergone an aquatic ecosystem transformation in response to 21st-century accelerated Arctic warming that is unparalleled in at least the past two centuries. Algal remains from a series of high-resolution palaeolimnological records retrieved from the West Basin provide baseline limnological data that we compared to historical limnological and phycological surveys undertaken on Great Slave Lake between the 1940s and 1990s. We document the rapid restructuring of algal community composition ca. 2000 CE that is consistent with recent increases in regional air temperature, as well as declines in ice cover and wind speed, that would collectively alter habitats for aquatic biota (e.g. thermal regime, vertical mixing, turbidity, light and nutrients). This new limnological regime initiated the first observation of scaled chrysophytes and favoured the rapid proliferation of small planktonic cyclotelloid diatoms that replaced the long-established dominance of large filamentous Aulacoseira islandica in West Basin sedimentary assemblages. Such rapid transformations in the primary producers of this socio-ecologically valuable “northern Great Lake” may have widespread implications for the entire food web with unknown consequences for aquatic ecosystem functioning and fisheries, which many northern and Indigenous communities depend upon.

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