Although recent ecological changes are widespread in Arctic lakes, it remains unclear whether they are more strongly associated with climate warming or the deposition of reactive nitrogen (Nr) from anthropogenic sources. We developed a 3500-yr paleolimnological record from the world’s northernmost lake to explore this question. Microfossils indicate that siliceous diatoms and chrysophytes were abundant initially, but disappeared 2400 yr ago in concert with Neoglacial cooling. Microfossils reappear in 20th-century sediments and reach unprecedented concentrations in sediments deposited after ca. A.D. 1980, tracking increasing summer temperatures in the absence of evidence for atmospheric nutrient subsidies. These results indicate that current warming in northern Greenland is unprecedented in the context of the past 2400 yr, and that climate change alone is responsible for the marked biological changes observed.