In this study, seasonal stable isotope compositions of zooplankton and particulate organic matter were analyzed from the coastal zone in Kepez Harbor, the discharge point of a waste treatment plant. The results were compared with the results of a control station located 10 km away from the harbor. Zooplankton samples were collected horizontally with a 200 μm mesh plankton net from the surface waters. POM samples were collected with a 5L Nansen bottle and filtered through precombusted GF/F filters. Variables such as temperature, salinity, chlorophyll-a as well as oil-grease and chemical oxygen demand were also determined in the study sites. The salinity values in the control station were significantly higher than the harbor station through the whole year. The δ¹³C values of POM in the control station were significantly higher than the values observed in the harbor station. The δ¹⁵N values of zooplankton in the harbor were higher than the values obtained in the control station; however, the differences were not significant. The values of oil-grease obtained in two stations were lower than the values pronounced in EPA, EU, and Turkish Regulations. The study showed that the stable isotope compositions were affected by terrestrial inputs and high currents rather than the facilities comprised in the harbor.