The effect of Black Sea Water (BSW) inputs on the productivity and food web dynamics of the N. Aegean Sea was investigated, by means of sensitivity simulations, investigating the effect of the inflowing BSW, in terms of inorganic nutrients and dissolved organic matter. Considering the importance of the microbial loop in ecosystem functioning and the role of dissolved organics, the bacteria sub-model was appropriately revised, towards a more realistic representation of the Dissolved Organic Matter (DOM) pool. The importance of the microbial loop is highlighted by the simulated carbon fluxes, where almost 50% of carbon is channelled within it. The impact of DOM (in the inflowing to the Aegean Sea BSW) appears to be stronger than the impact of dissolved inorganic nutrients, showing a more extended effect over the N. Aegean. Bacterial production and biomass is more strongly affected in the simulations by modified DOM, while phytoplankton biomass and production are more dependent on inflowing nutrients and particularly phosphorus (inorganic and dissolved organic). As regards phytoplankton composition, the dinoflagellates appear to be affected most, being favoured by higher nutrient availability at the expense of all other groups, particularly picoplankton, indicating a shift to a more classical food chain.