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Organic carbon (Corg) and total nitrogen (N) concentrations in combination with stable organic carbon (δ13Corg) and nitrogen (δ15N) isotopic composition were used to investigate the organic matter sources and influence of anthropogenic activities on recent sediments of eutrophic Lake Pamvotis (Greece) and oligotrophic Lake Bohinj (Slovenia). Corg and N concentrations increase upcore showing a progressive nutrient enrichment in both lakes. The C/N ratios vary with depth and indicate that allochthonous and autochthonous sources contributed to sedimentary organic matter. Never the less, an excursion to relatively low surface sediment C/N ratios suggests that recently the latter predominates. Finally, δ13Corg and δ15N records showed changes in carbon and nitrogen cycles related predominantly to local anthropogenic activities in Lake Pamvotis and to anthropogenic activities (i.e. woodcutting) and global atmospheric changes in Lake Bohinj.