This study describes the coupling between physical and biogeochemical models and analyses the response of the ecosystem in the north-western Black Sea to nutrient loads and climate changes. The basic physical and biological dynamics of the upper north-western Black Sea is illustrated as well. The physical model is based on the Princeton Ocean Model (POM); additionally, a parameterisation of mixed layer is included. The biogeochemical model is based on the European Regional Sea Ecosystem Model (ERSEM) and consists of five modules: (1) primary producers, (2) microbial loop, (3) mesozooplankton, (4) benthic nutrients, and (5) benthic biology. The ecosystem in ERSEM is subdivided into three functional types, producers (phytoplankton), decomposers (pelagic and benthic bacteria) and consumers (zooplankton and zoobenthos). Model-data comparisons have been performed for both calibrating and verifying coupled model simulations. We address here the impact of nutrient discharge from the Danube River on the functioning of the biological system. The evolution of the mixed layer, as well as the response of the biological system to variability of the nutrient discharge from the Danube River is described in detail. Several scenarios have been developed to study the impact which nutrient reduction has on the coastal marine system. The model predictions indicate that the biological system is very sensitive to the changes in nutrient concentrations, as well as to their ratios.