We report the results of tephrochronological studies on marine cores from the eastern and western part of the Sea of Marmara extending back to early MIS-4. Glass shard compositions using electron probe microanalyses (EPMA) and stratigraphic analysis assigned three distinct tephra layers to the eruption of Avellino (Somma-Vesuvius/Italy, 3.9 ka), Cape Riva (Thera/Santorini, 22 ka) and the Campanian Ignimbrite (Phlegrean Fields/Italy, 39.3 ka), respectively. Tephra layers are important chronostratigraphic markers for the refining of age–depth models of cores and thus for the reconstruction of the palaeoceanographic evolution of the Sea of Marmara. Accordingly, a continuous sedimentary record for the last ca. 67 ka in core MD01-2430, located at − 580 m on the Western High, shows only one lacustrine–marine transition at 12.55 ± 0.35 cal ka BP, which indicates that the Sea of Marmara was under lacustrine conditions disconnected from the Mediterranean Sea from early MIS-4 to early MIS-1. High lake levels and oxic bottom water conditions prevailed especially during the MIS-3 stadials. This implies that the sill depth of the Çanakkale Strait (Dardanelles) was probably higher during MIS-3 time than the present sill depth of − 65 m. Alternatively, strong fresh water discharges from the Black Sea during the interstadials might have kept the Sea of Marmara stratified with a relatively thick layer of fresh waters above a weak Mediterranean inflow filling only deeper parts of the basins.

Based on the radiocarbon and tephra-integrated age model the marine transgression at 12.55 ± 0.35 cal ka BP was followed by the deposition of the main lower Holocene sapropel between ca. 12.3 and 5.7 cal ka BP, and in the shallow shelf areas (<~100 m depth) such as the Gemlik Gulf, by the formation of the upper Holocene sapropel between ca. 5.4 and 2.7 cal ka BP.