Implementation of the EU Water Framework Directive will call for new lake monitoring and management strategies. Therefore, different methods need to be tested in order to achieve reliable assessment of lake background conditions and water quality. Sediment-based techniques provide one such tool for lake management. In this work, 10 lakes, presumed to be naturally eutrophic, were investigated with a paleolimnological short core study. The aim of the study was to examine the composition of the diatom assemblages in their natural state, estimate their change over time and assess the background nutrient levels. One sediment profile from each lake was divided into six sub-samples that were analyzed for diatoms (60 samples). Diatom-based inference models were applied to reconstruct the past total phosphorus concentration and assess the eutrophication. The results indicated that all the lakes studied had already been nutrient-rich before the impact of modern agriculture. However, diatom assemblages have changed remarkably over time and total phosphorus concentrations have generally increased, so at present only two of the study lakes are close to their natural status. This suggests that naturally eutrophic lakes will probably require management actions to fulfill the new directive requirements in the future.