Management authorities often perceive Didymosphenia geminata (didymo) as an invasive, nuisance diatom species that has been introduced to eastern Canada; however, observations from early 20th century diatom surveys challenge this characterization. We apply paleolimnological techniques to place recent didymo blooms from Gaspésie, Quebec, into historical and environmental context. Sedimentary diatom assemblages were examined from Lac Humqui (a headwater lake) and Lac au Saumon (a lake with an inflowing river currently supporting blooms). The Lac Humqui assemblage experienced a broad-scale shift in their dominant life strategy with declines in fragilarioid taxa and increases in planktonic diatoms (i.e., Cyclotella–Discostella species) that began ∼1970 and increased to modern abundances ∼1990. Strong relationships between this diatom shift and increases in regional air temperatures and earlier river ice-out dates are consistent with longer growing seasons and enhanced thermal stability in Lac Humqui. Didymo was observed throughout the Lac au Saumon core, demonstrating that it has been present in the region since at least ∼1970. Our paleolimnological evidence indicates that blooms likely form in response to regional consequences of climate warming, rather than human introduction.