The dynamics of the phytoplankton community were studied along the Montenegrin coast, in the mesotrophic area of Boka Kotorska Bay and the oligotrophic coastal open sea area. This two year study investigates differences in dynamics of phytoplankton assemblages and abundances in the Bay area, which is highly impacted from the land, and the open coastal part of the Montenegrin coast, which is highly influenced by Levantine water masses but less affected by anthropogenic influence.` Regarding phytoplankton diversity, the microplankton species detected are those that prefer areas rich in inorganic nutrients, such as Chaetoceros affinis, Dactyliosolen fragilissimus, Leptocylindrus danicus, Pseudo-nitzschia spp., and Thalassionema nitzschioides. These species used both new and regenerated nutrients which regenerated at each grazing level of the microbial loop and are thus made available to the primary producers. The potentially toxic Pseudo-nitzschia spp. reached an abundance of 105 cells/L. Among the potentially toxic dinoflagellates, Dinophysis acuminata, D. acuta, D. caudata, D. fortii, D. tripos, Gonyaulax spinifera, Lingulodinium polyedra, Phalacroma rotundatum were recorded (the abundance reached values up to 102 cells/L). The detected presence of several potentially toxic and toxic phytoplankton species warrants the need to raise awareness for the necessity of continuous monitoring activities and preventive measures.