Bosphorus and Dardanelles form the Turkish Straits System together with the Marmara Sea. The system provides a connection between the Mediterranean and the Black Sea. Istanbul and its coastal environment have been strongly affected by wastewater discharges, high population and heavy ship traffic. The aim of this study is to provide a comparison between the chemical and biological analysis of surface sediment samples, which were collected from 17 different coastal stations of the Istanbul Strait, to determine the pollutants and comparable effect related data. For the chemical analysis, PAH, PCDD/F and PCB isotope dilution techniques, and for the biological analysis, Micro EROD (24-h and 72-h) assay were employed. Highest values were found at the most polluted sites due to ship traffic and wastewater discharges. Most of the results of chemical analysis were lower or close to biological analysis, except for the samples from two stations where antagonistic modulators are indicated to be present in the Micro EROD assay. This study suggests that the WWTP discharges into Bosphorus and the heavy ship traffic are important sources of pollution in the sediment, as evidenced by high concentrations of toxic and persistent organic chemicals. Local discharges of the megacity should be further decreased.