In the surface layer of the Sevastopol and Quarantine bays, during 2000–2014 in summer and in autumn, the average values of the concentration of chlorophyll a and phytoplankton biomass are reduced by a factor of 2–5. This is due to a decrease in the content of nitrates and silicon compounds in water, as well as the relative proportion of diatoms in the total biomass of phytoplankton. Regression analysis showed that in the summer period the long-term negative trend in the change in the relative biomass of diatoms was determined mainly by the nitrate content in the water and its temperature, while in the autumn – by the content of nitrates and silicon. The share of dinoflagellates and coccolithophores increased over the entire observation period. In winter and spring in bays, and in the open coast during all seasons, unidirectional changes in the concentration of chlorophyll and the total biomass of phytoplankton were not detected.