The Black sea is a deep semi-enclosed dilution basin connected with the Mediterranean Sea by shallow and narrow Turkish Straits with hydraulically controlled two-layer water exchange. The simulation of sea level, temperature and salinity change in the Black Sea in 2000-2100 was carried out using a chain of models, which includes models of the Black and Azov Seas, as well as the Kerch Strait, the Turkish Straits (Bosphorus and Dardanelles) and the Marmara Sea models. The air temperature, wind, evaporation and precipitation for period 2000-2100 over the Black Sea and its catchment area was calculated from regional model CNRM-ALADIN (MED-11) modeling data for RCP4.5 and RCP8.5 scenarios. The neural networks were used to obtain components of freshwater budget from regional model simulations, whereas boundary conditions (sea level, temperature and salinity) in the North Aegean Sea were used from CMIP5 model CNRM CM5.1. The calculated trend of the sea level for period 2000-2100 (3.6 mm/y and 4.6 mm/y for RCP4.5 and RCP8.5, respectively) is close to the corresponding trends in the Mediterranean Sea. The steric correction almost compensates sea-level fall due to the decrease of freshwater influx at 85 km3/y and 99 km3/y in 2100 for RCP4.5 and RCP8.5, respectively. Increasing the air temperature over the sea and reducing the inflow of fresh water are the major factors in changes in the surface layer of the Black Sea. In the period 2000-2100, water temperature of the surface layer of the Black Sea will increase by 2.7 oC, the salinity by 1.7 for the scenario RCP4.5, while the corresponding values will increase by 4.1 oC and by 1.75 for the scenario RCP8.5. These changes in the physical characteristics of the Black and Azov Seas can have a significant impact on the ecosystem of these basins, shores and coastal infrastructure.