The Sea of Marmara is the connection between the vast Black Sea-Caspian Sea basin (Pontocaspian) and the Global Ocean via the Mediterranean Sea. Its water levels and water conditions has widely varied over times. Combining two cores in the Sea of Marmara (Turkey) and using organic-walled dinoflagellate cyst assemblages as the main proxy (combined with alkenones, diatoms and benthic foraminifera), allow qualitatively reconstructing water conditions during Marine Isotopic Stage (MIS) 6 and 5, such as salinity and oxygen level. A clear main marine phase is illustrated in MIS 5e. A minor marine incursion occurred during MIS 5c, mostly supported by alkenone data. The rest of the record indicates brackish Pontocaspian conditions, with more Spiniferites inaequalis in MIS 6 and more S. cruciformis in the non-marine parts of MIS 5.

At the MIS 6/MIS 5 transition, an earlier initial marine flooding in the Sea of Marmara (dinocyst assemblages) in comparison to the Black Sea was highlighted. The marine reconnection occurred at different moments as seen in the terrestrial vegetation reconstructed from pollen analysis linking the two seas.

The sapropels of the Sea of Marmara form when marine water penetrates at depth from the Aegean Sea beneath a layer of lower salinity water. Variations of the residence time of the marine deep water in a stratified Sea of Marmara are potentially an important factor underlying hypoxia/anoxia and sapropel deposition. When combining surface water proxies with benthic foraminifera (test assemblages and presence of inner organic lining), it appears that the successive MIS 5 sapropels formed under decreasing salinity and oxygen availability conditions as the marine inflow was increasingly restricted. Understanding the hydrologic evolution of the Sea of Marmara during MIS 5 implies taking into account that the Bosphorus and Dardanelle straits are hydrodynamically coupled and may not be simplified as on/off switches based on present day sill depths.