In the last decade, sea bass and gilthead sea bream aquaculture had an exponential growth in the Mediterranean region, however, little detailed information is available on the environmental impacts of this industry. In general, it has been assumed that impacts will, at least qualitatively, follow the pattern established in northern latitudes. The Mediterranean environment is, however, profoundly different to northern temperate seas as regards temperature, salinity, tidal energy, biota and trophic status and this modifies the processes involved in assimilating organic wastes. We are researching the physical, biological and chemical effects of cage farming at several sites around Greece within a modelling framework to provide modelling and monitoring tools for the environmental management of this industry. We aim at parameterising an existing Scottish model for Mediterranean conditions taking into account the different cultured fish species and processes such as the scavenging of carbon from the immediate locality by wild fish and epifauna.