In the framework of EU-MC project SIMSEA, a modelling study has been initiated to validate the General Estuarine Transport Model (GETM) for Black Sea’s simulations. The model is forced with atmospheric data from the European Regional Downscaling Experiment (EURO-CORDEX), river runoff from Global Runoff Data Centre (GRDC) and is initialised with temperature and salinity 3D fields coming from the project MEDAR/MEDATLAS II. Simulations are performed in a closed basin configuration with boundary conditions at the Bosphorus strait ensuring a net zero water flux balance in the Black Sea. An accurate method to calculate the optical depth estimated from satellite data has been involved. The model has been validated against measured/calculated temperature and salinity fields. The simulations with our hydrodynamic model correctly capture the Black Sea’s hydrodynamics – the strong halocline at 70-150 m, the Cold Intermediate Layer (CIL) at ~70 m, the doming of the isohalines due to the cyclonic Rim current, sea surface temperature variation, etc. A new Black Sea Ecosystem Model (BSSM) is linked via the Framework for Aquatic Biogeochemical Models (FABM,) with our hydrodynamic model. The coupled physical-ecosystem modelling system has been also calibrated and validated for the Black Sea runs. The numerical experiments indicate that the biogeochemical components of the model rather successfully reproduce the main features and state variable evolution in the Black Sea ecosystem: the growth in phytoplankton biomass and changes in seasonal cycles of the main ecosystem components. It is concluded that the physical processes are important for a reliable reproduction of seasonal and inter-annual changes in the ecosystem.