Chirp sub-bottom profiling, multibeam bathymetric mapping and a combination of faunal and isotopic analysis of molluscs and foraminifera in sediment cores on the northern shelf of the Sea of Marmara (SoM) provide evidence of sea-level excursions, water exchanges between the adjacent Mediterranean and Black Seas, and oscillating salinity over the last 160 ka bp. During the marine isotope stages MIS-2, MIS-3, MIS-4 and MIS-6 the SoM disconnected from the Mediterranean Sea and evolved into a lake. During MIS-1, MIS-5 and MIS-7, the SoM reconnected and became salty once again. Sapropels formed shortly after each invasion of Mediterranean saltwater observed in our cores. Concurrent suboxic-dysoxic conditions prevailed over quite shallow substrates on the shelf.