In addition to food supply, there is a growing recognition of the wider ecosystem benefits of Integrated Multitrophic Aquaculture (IMTA) systems in coastal waters, including regulating services such as carbon sequestration and nutrient remediation. The water trophic status and the co-cultured species combinations affect IMTA productivity. In this study, we examined the ability of different combinations of IMTA organisms to remediate nutrients and the economic/environmental gain for reducing the environmental footprint in potential IMTA systems of the eastern Mediterranean. The results showed that the co-cultivation of organisms can reduce the negative effects on the marine environment of a fish farm both on the water column and the sediment. Meso- and eutrophic water states do not show a high variation in terms of foot print mitigation, with all three of the co-cultivated organisms to perform well. In oligotrophic waters, the obligatory absence of mussels reduces the effectiveness of the IMTA system. As expected, larger-sized IMTA systems have higher production rates and as a result higher percentage of nutrient removal. Finally, bivalve harvesting helps to remove the carbon that is trapped in their shells, contributing to the mitigation of processes related to climate change, such as the acidification of the oceans.