Spatial and temporal distribution of benthic communities around the Strait of Istanbul (Bosphorus) and the effect of lower layer discharge on these communities have been evaluated during studies between February-December 1999. Mytilus galloprovincialis was the dominant species with fasies at the Black Sea station that is not affected by the strait lower layer current system. On the other hand, another Black Sea station, influenced by the strait lower layer currents, has a similar biota to the strait stations. Species richness and diversity is highest in the strait than other areas. The dominant species is Maera grossimana. However, the station located at the Black Sea exit of the strait has a different biota, and various groups/species appeared to be dominant. Melinna palmata is the dominant species at the Sea of Marmara during the study period. Low dissolved oxygen values of lower layer and soft substratum of sediment resulted in wide distribution of Melinna palmata, adapted to these conditions. The closer stations to the strait in the Sea of Marmara have higher diversity as a result of hydrodynamic processes. On the other hand, coastal stations with low currents and inputs have lower index values, showing the negative effect of discharges and pollution.