Abstract Surficial sediments and mussels ( Mytilus galloprovincialis) from the Istanbul Strait and Marmara Sea were analysed for sixteen parent polycyclic aromatic hydrocarbon (PAH) contents by gas chromatography-mass spectrometry (GC-MS) employing isotope dilution technique. Microalgae toxicity testing was applied to sediment elutriates and biological responses in terms of filtration rate and lysosomal stability were measured in mussels. Total PAH concentrations ranged from 2.1 to 3152 ng g − 1 dry wt in sediments and from 43–601 ng g − 1 wet weight in mussels. Molecular indices of phenanthrene/ anthracene, fluoranthene/pyrene and benzo(a)anthracene/chrysene were used to differentiate between pyrolytic and petroleum origin. Results showed that most of the contamination originates from high temperature pyrolytic inputs with some slight contribution of petrogenic PAH. PAH in sediments were frequently lower than the National Oceanic and Atmospheric Administration (NOAA)–ERM (Effects Range Medium) index. Results of sediment elutriate toxicity testing and biomarkers indicate that the cause of negative effects in sediments may result from different classes of pollutants and does not only relate with PAH contamination. Mussels from most of the stations showed both reduced lysosomal membrane stability and filtration rate indicating disturbed health although the two biomarker results did not always complement each other. The effect studies showed that the pollutants in the strait ecosystem have more pronounced effects in the middle parts than those at the Black Sea entrance.