The winter peak of phytoplankton bloom in the Sevastopol Bay is reproduced using the 3D water quality model MECCA using meteorological data for January 2003. A detailed dynamic pattern of currents' variability, temperature, salinity, concentration of phytoplankton biomass and phosphate phosphorus is reproduced. The formation of an anticyclonic eddy in the central region of the bay is demonstrated, which led to an increase in the phosphorus phosphates concentration and phytoplankton bloom. The maximum of phytoplankton bloom (0.056 gC/m³) was observed on the 23rd model day in the central part, then the maximum concentration of biomass decreased to 0.047 gC/m³ in the central and eastern parts of the bay. There was also a decrease in phosphorus phosphates concentration from the maximum 0.0085 gP/m³ on January, 10 to 0.0049 gP/m³ on January, 23 in the central part of the bay. The concentration of phytoplankton biomass increased until January, 23, and then decreased, the phosphorus phosphates concentration decreased throughout the whole calculation period. The estimates obtained in the course of numerical modelling generally agree with the observational data. The performed study can serve as a basis for the development and application of a model approach to monitoring and managing of ecosystem processes on shallow water. Using this model, it is possible to calculate various scenarios for the bay eutrophication in case nutrients are discharged.