Subfossil biotic assemblages in surface sediments of lakes have been used to infer ecological conditions across environmental gradients.. Local variables are usually the major drives of assemblage composition, but in remote oceanic islands biogeographic filters may play a significant role. To assess the contribution of local and regional filters in the composition of subfossil diatoms and chironomid assemblages in surface sediments forty-one lakes in Azores archipelago ()were studied and related to environmental variables. Ordination techniques were used to identify the drivers that best explain the composition of these assemblages. Both assemblages are influenced by multiple limnological variables (conductivity, pH, nutrients). However, diatom assemblages differed mainly in the proportion of planktonic versus benthic species along the lakes' depth gradient while Chironomids differed significantly between islands but not between lake depths.. Thus, biogeographic filters play an important role in shaping islands freshwater communities, particularly insect ones, more influenced by geographic variables. Results demonstrate the accuracy and potential of biotic remains in sediments for applied studies of lake ecology, trophic status, climatic trends and ecological reconstruction and evolution of lakes. In the Azores, the application of this information in the development of inference models, is envisaged as further step to accomplish these goals.