Benthic habitat at the continental shelf area of the Marmara Sea is strongly affected by the confluence of the saline Mediterranean and brackish Black Sea waters. Benthic foraminiferal composition and abundance (undifferentiated living and dead) in 19 surface sediment samples taken from water depths between 15 and 67m from the northern Marmara shelf was studied as tracers of the Mediterranean and Black Sea water masses in the area. Faunal analysis showed that a distinct change occured at about 40m water depth. Two main assemblages were identified based on cluster analysis of the quantitative benthic foraminiferal data. They are the Asterigerinata mamilla-Lobatula lobatula-Neoconorbina terquemi assemblage (Shallower assemblage) at 20-38m water depth and Brizalina spathulata-Cassidulina carinata-Bulimina aculeata assemblage (Deeper assemblage) distributed at 43-67m. Comparison between the depth distribution of representative species and basin-averaged salinity gradient clearly shows that faunal shift follows the hydrological boundary.