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We study the seasonal variability of the Black-Sea ecosystem by using a three-dimensional physical-biogeochemical model. Its physical part is a model of circulation in the Black Sea with high spatial resolution capable of the description of both large-scale circulation in the basin and mesoscale eddies. The ecological module of the model is based on a version of the already applied one-dimensional model generalized to the three-dimensional case and includes two components of phytoplankton, two groups of zooplankton of different sizes, bacteria, dissolved and suspended organic substances, jointly described nitrates and nitrites, and ammonium. The application of the eddy-resolving model as the basic model of circulation in the Black Sea enable us to qualitatively reproduce the processes of vertical entrainment of deep-sea waters rich in biogenic elements into the upper layer and transfrontal transport of the coastal waters into the open part of the sea. Our numerical experiments also demonstrate that this model realistically reproduces the seasonal dynamics of the distribution of phytoplankton in the Black Sea. In addition, the model reproduces the space structure of the biogeochemical variables of state correlated with the mesoscale features of circulation.[PUBLICATION ABSTRACT]