A three-dimensional integrated mathematical model, ModEling aquacultures-Sea environment Interactions (MESI), is presented to describe the interactions between aquacultures and the sea environment and to evaluate the environmental effects on the coastal waters due mainly to the non-utilized fish food originating from the aquacultures. The model consists of three sub-models: (1) a fish growth and nitrogen and phosphorus transformation sub-model for the calculation of the growth of the fishes and the generated loads of pollutants, (2) a hydrodynamic sub-model for the determination of the flow field in the coastal region and (3) a water quality model to determine the concentration contours of the water quality variables in the coastal region. The application of the model to a coastal area of simple geometry containing an aquaculture demonstrates its ability to evaluate the effects of the aquaculture on the coastal waters.