Present-day bottom-water ventilation in the Eastern Mediterranean basin occurs through deep-water convection originating from the two marginal basins, i.e. Adriatic and Aegean Seas. In the paleo record, long periods of enhanced deep-water formation have been alternating with shorter periods of reduced deep-water formation. The latter is related mainly to low-latitude humid climate conditions and the enhanced deposition and preservation of organic-rich sediment units (sapropels). This study focuses on sedimentary archives of the most-recent sapropel S1, retrieved from two sites under the direct influence of the two deep-water formation areas. Restricted oxygen conditions have developed rapidly at the beginning of S1 deposition in the Adriatic site, but bottom-water conditions have not persistently remained anoxic during the full interval of sapropel deposition. In fact, the variability in intensity and persistence of sedimentary redox conditions at the two deep-water formation sites is shown to be related to brief episodes of climate cooling. In the Adriatic site, sapropel deposition appears to have been interrupted twice. The 8.2 ka event, only recovered at the Adria site, is characterized by gradually increasing suboxic to possibly intermittently oxic conditions and decreasing Corg fluxes, followed by an abrupt re-establishment of anoxic conditions. Another important event that disrupted sapropel S1 formation, has taken place at ca. 7.4 cal ka BP. The latter event has been recovered at both sites. In the Adriatic site it is followed by a period of sedimentary conditions that gradually change from suboxic to more permanently oxic, as deduced from the Mn/Al pattern. Using the same proxy for suboxic/oxic sedimentary redox conditions, we observe that conditions in the Aegean Sea site shift to more permanently oxic from the 7.4 ka event onwards. However, at both sites the accumulation and preservation of enhanced amounts of organic matter have continued under these suboxic to intermittently oxic sedimentary conditions. It seems thus, that after 7.4 cal ka BP sapropel-like surface or deep-chlorophyll-maximum conditions including enhanced productivity continued, whereas bottom-water conditions were at least intermittently oxic. The latter is related to decreasing precipitation, i.e. run-off, and thus a progressive development and deepening of deep-water formation. The shallower Aegean site, would be affected earlier by such deepening ventilation than the slightly deeper Adriatic site. Finally, termination of sapropel S1 formation as deduced from diminished organic matter contents and Ba/Al, appears to have occurred almost simultaneously in the two areas, namely at 6.6 ± 0.3 and 6.3 ± 0.5 cal ka BP in Adriatic and Aegean sites, respectively.