Abstract. A three dimensional coupled physical-biological model is provided for the Black Sea to investigate its long-term changes under the synergistic impacts of eutrophication, climatic changes and population outbreak of the gelatinous invader Mnemiopsis leidyi. The model circulation field is simulated using the high frequency ERA40 atmospheric forcing as well as assimilation of the available hydrographic and altimeter sea level anomaly data for the 30 yr period of 1971–2001. The circulation dynamics are shown to resolve well the different temporal and spatial scales from mesoscale to sub-basin scale and from seasonal peaks to decadal scale trend-like changes. The biogeochemical model includes the main vertical biological and chemical interactions and processes up to the anoxic interface zone. Its food web structure is represented by two phytoplankton and zooplankton size groups, bacterioplankton, gelatinous carnivores Mnemiopsis and Aurelia, opportunistic species Noctiluca scientillans. The nitrogen cycling is accommodated by the particulate and dissolved organic nitrogen compartments and the dissolved inorganic nitrogen in the forms of ammonium, nitrite and nitrate. The ecosystem model is able to simulate successfully main observed features and trends of the intense eutrophication phase (from the early 1970s to the early 1990s), but points to its modification to simulate better the ecosystem conditions of the post-eutrophication phase.