We evaluated foraminiferal data from Holocene borehole samples of the Golden Horn (Istanbul, NW Turkey) and the extrinsic factors controlling the distribution of microfaunas of the seaway system connecting the Golden Horn to the Black and Aegean seas. Samples were collected along two different transects: one transect to the west between Unkapani and Azapkapi and a second transect to the east between Eminonu and Karakoy. Foraminiferal species distribution, abundance, and diversity exhibit a range of conditions from brackish to shallow-water marine paleoenvironments during the last 7400 years. The lithologic composition, sedimentologic features and palynologic data indicate that freshwater paleoenvironments existed before the present marine conditions. Haurinid species are more abundant than rotaliids to the west (Unkapani-Azapkapi transect), where gypsum crystals are also present; rotaliids dominate to the east, while textulariids are rare. Some typical foraminifera such as Laevipeneroplis, Peneroplis, Sorites and Amphistegina are of Mediterranean origin. Observations on Middle and Upper Holocene sediments prior to the last century were related to non-polluted sediments including foraminifera and other fauna. However, anthropogenic effects during the last century caused the fauna to disappear from the polluted area. Foraminifera are now being found again in the Golden Horn embayment after the institution of anti-pollution measures. (C) 2006 Elsevier Ltd. All rights reserved.