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Decline of the river Don runoff to its historic minima, as well as intensive cyclonic activity and abnormal advection of the Black Sea waters led to the fact that in 2014-2016, very high salinity values (up to 12 psu) were observed in the Taganrog Bay. Under certain hydrometeorological conditions, salt water can penetrate deep into the river Don mouth. Therefore, study of changes in the Azov Sea hydrothermodynamics is rather an actual problem, which is proposed to be solved by numerical modeling. Methods and Results. The paper represents the methodology for carrying out long-term model runs for joint dynamics of the Black, Azov and Marmara seas based on the eddy-resolving configuration of the NEMO modeling framework. A new-generation ERA5 reanalysis with a sufficiently high spatial resolution was used for the first time as a atmospheric forcing for the region. New information on the rivers Don and Kuban' runoffs were used and adjustment simulations were done to obtain the initial conditions. The results were verified based on the data from coastal hydrometeorological stations in the Sea of Azov. Some results of model simulations for the period from mid-2007 to 2016 are represented. A positive salinity trend in the basin of the Azov Sea is well pronounced. Surface boundary conditions for the heat flux were corrected for the purpose of carrying out simulations without ice modeling and reproducing adequate temperature values of the Azov Sea waters. Conclusions. The performed numerical experiments showed applicability for the developed model regional configuration to further investigations. However, more detailed analysis of the results obtained for the Black Sea basin is required. Consideration of the basic external conditions in modeling made it possible to reproduce positive tendency of salinity in the Sea of Azov. The temperature simulation results indirectly agree with the sea ice data.