We investigated potential effects of the fish farms on water column and sediment around Salih Island in the Gulluk Bay (Aegean Sea, Turkey) where four seasonal samplings were performed from October 2001 to August 2002. One measured physicochemical variables in water column including dissolved oxygen, nutrients (nitrite, nitrate, ammonium, phosphate and silicate), particulate organic carbon (POC) and chlorophyll a. Organic matter, total organic carbon (TOC) and heavy metals (Zn, Cu and Fe) were measured in sediment samples. Although occasional increases in ammonium and chlorophyll a concentrations were observed at the cage stations as compared to the control one, no statistically significant differences were detected among the stations in terms of nutrients, chlorophyll a and POC. On the other hand, significant differences were found in organic matter, TOC and heavy metals (Zn and Fe) of the sediments among the sampling stations. Despite these differences, our results indicate that concentrations of physicochemical variables and heavy metals were within the range of tolerable levels for the marine ecosystem, and the oligotrophic nature of the water column in the study area was able to assimilate organic and inorganic loads caused by the fish farms.