Late glacial to Holocene paleoclimatic and paleoceanographic changes are examined using records of calcareous and organic-walled marine microfossils, pollen and terrestrial spores and oxygen isotope data in cores from the Aegean Sea basins. Planktic foraminiferal, coccolith and dinoflagellate data show that the late glacial-Holocene transition in the region was associated with a large warming of surface water. Mediterranean-based paleotransfer functions for planktic foraminifera show a 5 degrees-10 degrees C increase in surface water temperature from similar to 14,000 to similar to 9600 yr B.P. Estimates of surface water oxygen isotopic composition (delta(18)O(w)) derived from planktic foraminiferal oxygen isotopic and transfer function data indicate that this warming was associated with a 2.0 to 2.5 parts per thousand reduction in delta(18)O(w). Transfer function results indicate corresponding 1.0 to 1.5 parts per thousand salinity reductions for this time (ca. 9600-6400 yr B.P.) throughout the Aegean Sea. Pollen, dinoflagellate and isotopic data show that the early Holocene excess fresh water originated from rapid melting of the northern European and Siberian ice sheets,supplied primarily from the Black Sea by the opening of Bosphorus and Dardanelles Channels, during the post glacial sea-level rise, and supplemented by major rivers entering the Aegean Sea, Continuous outflow of fresh water into the Aegean Sea provided a low salinity surface lid, preventing the ventilation of the deep water. Benthic foraminifera shows a major turn-over that indicates low dissolved oxygen; however, bottom waters were not anoxic. Sapropel level S1 resulted from a combination of stagnant deep water in isolated depressions, increased terrigenous organic matter and periods of high primary productivity, as indicated by pollen and dinocysts, respectively. The surface water temperature and salinity reached present-day values at similar to 6400 yr B.P., with little subsequent change despite the major deforestation onshore.