Sediments deposited under lacustrine and marine conditions in the Sea of Marmara hold a Late Quaternary record for water exchange between the Black Sea and the Mediterranean Sea. Here we report a multiproxy data set based on oxygen and strontium isotope results obtained from carbonate shells, major and trace elements, and specific organic biomarker measurements, as well as a micropaleontological study from a 14C‐dated sediment core retrieved from the Sea of Marmara. Pronounced changes occurred in δ18O and 87Sr/86Sr values at the fresh and marine water transition, providing additional information in relation to micropaleontological data. Organic biomarker concentrations documented the marine origin of the sapropelic layer while changes in n‐alkane concentrations clearly indicated an enhanced contribution for organic matter of terrestrial origin before and after the event. When compared with the Black Sea record, the results suggest that the Black Sea was outflowing to the Sea of Marmara from the Last Glacial Maximum until the warmer Bølling‐Allerød. The first marine incursion in the Sea of Marmara occurred at 14.7 cal ka B.P. However, salinification of the basin was gradual, indicating that Black Sea freshwaters were still contributing to the Marmara seawater budget. After the Younger Dryas (which is associated with a high input of organic matter of terrestrial origin) both basins were disconnected, resulting in a salinity increase in the Sea of Marmara. The deposition of organic‐rich sapropel that followed was mainly related to enhanced primary productivity characterized by a reorganization of the phytoplankton population.