The historical Golden Horn Estuary (GHE), near the confluence of the Istanbul Strait (Bosphorus) and the Sea of Marmara in the European part of Istanbul, has been used as a natural harbor since 330 A. D. The sedimentary infill of the GHE is 15-46 m thick, deposited unconformably above the turbiditic sandstones of the Carboniferous Trakya Formation. Chronostratigraphic and paleontological analyses of the infill sequence indicate that the GHE was a fluvial channel prior to 13,500 cal. a (calibrated to calendar years) B. P. It subsequently became gradually influenced by marine waters, and was a brackish-water environment until 9,500 cal. a B. P. Normal marine salinities prevailed at ca. 9,500-5,600 cal. a B. P., with suboxic/dysoxic bottom-water conditions. The increase in salinity at 9,500 cal. a B. P. was most likely caused by Mediterranean water outflow into the Black Sea through the Istanbul Strait. The estuary was influenced by large fluvial inputs between 5,600 and 1,000 cal. a B. P., possibly during a distinct pluvial period, as shown by coarse siliciclastic sediments deposited on the flanks. It has become a highly polluted environment with marked anthropogenic inputs during the last millennium. The finding that the sediment infill sequence above the Carboniferous basement is not older than about 20 ka strongly suggests that the Golden Horn Estuary acquired its present-day morphology during the late glacial-Holocene period.