The freshwater diatom flora from arctic and subarctic regions of North America remains poorly known. The aim of this investigation is to improve our knowledge of diatoms in lakes from eastern subarctic Canada, and to provide a stronger foundation for the use of diatoms in limnological and palaeolimnological studies. To this end, we analysed the modern diatom assemblages in surficial sediments from 123 lakes in northern Québec and Labrador. The two study transects in Jamésie-Hudsonie (data set including 59 lakes and 38 environmental variables) and in Québec-Labrador (data set consisting of 64 lakes and 29 environmental variables) extend over a vast area from the boreal forest in the south to arctic tundra conditions in the north. Of a total of 516 diatom taxa in the Jamésie-Hudsonie data set, 218 species were used for the development of a transfer function for the reconstruction of dissolved organic carbon (DOC). In the Québec.Labrador data set, two inference models were developed for the reconstruction of water colour and alkalinity based on 128 of 303 diatom taxa. The majority of taxa belonging to this surprisingly species-rich boreal-subarctic diatom flora are illustrated in photographic plates, accompanied by a short description of the distribution of each taxon.