Capture-based aquaculture of Atlantic bluefin tuna in the Mediterranean has been expanding rapidly but little is known about its environmental impact. In order to understand the consequences of this new sector, long-term monitoring is needed. For this purpose, we investigated the impact of a capture-based tuna farm located in the Gerence Bay (Aegean Sea) on the water column on a seasonal basis from 2005 to 2008, where in the water column, temperature, salinity, pH, dissolved oxygen, nutrients (nitrite, nitrate, ammonium, and phosphate), and chlorophyll a, in the sediment organic carbon variables were measured. Although highest nutrient concentrations were observed at the cage station as compared to the two controls in the production period, differences were not statistically significant between stations. Monitoring of physico-chemical parameters, nutrients, and chlorophyll a in water column together with organic carbon in sediment did not show detectable impact of fattening of Atlantic bluefin tuna. This was probably caused by strong currents present in the area, location of the cages away from the coast, hence high water depth, controlled feeding, and periodic presence of tuna farming activity in the study area.