Qualitative and quantitative phytoplankton compositions of 10 Montenegrin lakes were investigated in the summer of 2007. The obtained results were compared with a previous study-period that was undertaken two decades ago. In the first period, diatoms numerically dominated the phytoplankton community in all studied lakes, while in the second period, the same was observed only in three of the ten lakes; in other studied lakes the relative contributions of green algae, dinoflagellates and/or cyanobacteria increased, while the contribution of diatoms decreased. The shift observed in phytoplankton composition and diversity in some of the studied lakes indicates an increase in the trophic level over the two decades. The sustainable management plan of the aquatic ecosystems in Montenegro should include the establishment of an environmental monitoring system in order to record any alterations that may take place in water quality.