A geochemical study of modern sediments across the Gulf of Gemlik in the Marmara Sea, Turkey, was carried out to investigate the main controls on the distribution of anthropogenic pollution. The textural composition, organic carbon content, heavy metal and PAH distribution, and their cause-result relationships from a total of 72 samples (from 6 to 320 m water depths) have been studied. In order to assess the relative importance of productivity, organic carbon accumulation and preservation, the results were compared with two sets of historical data covering the periods of 1990 and 1997. The eastern and southern coasts are mainly influenced by rapid industrial development, making this semi-enclosed embayment one of the most polluted hot spots in the Marmara Sea; an inland sea connecting the Black Sea to the Aegean Sea via the Turkish straits. Foraminiferal density and species richness of the assemblages decrease with an increase in heavy metal and PAH concentration and therefore may be used as pollution indicators. The more polluted areas are dominated by the tolerant pioneer species Amonia tepida and possibly Ammonia compacta and Elphidium crispum that may be used as bio-indicator of pollution, mainly in the inner part of the embayment and in the harbors.