The results of a study of the structural and functional characteristics of phytoplankton in the coastal region of the Black Sea using flow cytometry are presented. The data on the seasonal variability of the biomass of three algal groups (Synechococcus, pico-eukaryotic phytoplankton, and nanophytoplankton), chlorophyll a content, percentage of living cells, and FDA (diacetate fluorescein) fluorescence characterizing the functional state of algae are obtained. A significantly positive relationship is found between the values (biomass and autofluorescence of chlorophyll) determined on the flow cytometer and the total content of chlorophyll a, calculated using standard methods. The effect of temperature, illumination, and content of nutrients in water on the biomass and the FDA fluorescence of three isolated groups of algae is shown. The nitrate content and temperature have no significant effect on the abundance of pico and nanophytoplankton, while a reliable relationship is established between the biomass of nanophytoplankton and the concentrations of dissolved forms of mineral phosphorus. An inverse statistically significant correlation is found between the light intensity and the biomass of picoeukaryotic phytoplankton. It is demonstrated that the abiotic environmental factors considered in the study do not significantly affect the FDA fluorescence value, except for temperature: in the warm period of the year, the picophytoplankton are most active in the Black Sea, while the cold period of the year is favorable for the development of nanophytoplankton.