The hypothesis that the presence of fish farming zones affects the water quality and plankton communities was investigated in an Aegean Sea fish farm during February, June, September and January 2000–2001. In the spatial coverage, a total of 12 stations were sampled; three of them were reference stations. A variance analysis was applied to the measurements made at the stations near the fish farms and at the control stations. While no significant differences in concentrations of nutrients, chlorophyll a, particulate organic carbon and particulate organic nitrogen were detected between the stations and the control sites within one season, significant differences were detected between the parameter values measured except for total dissolved phosphorus and dissolved organic phosphorus at different seasons. The seasonal differences were also significant with regard to the biodiversity. Together with these temporal differences in general, there was a higher diversity of species at the control site as compared with the other stations in September, which was the key season to detection of significant changes. The most important consideration is that it is not sufficient to take the instantaneous values for the physico-chemical variables; rather, it is necessary to monitor the biological parameters in order to define the differences in the ecosystem.