Eastern Mediterranean thermohaline circulation is directly influenced by middle‐ and low‐latitude climate systems. The dramatic paleoclimate changes during the last African Humid Period (~10–6 ka BP) were captured in Mediterranean sediments as the distinctly organic‐rich unit sapropel S1. Here, deepwater formation variability during S1 deposition is reconstructed. We use geochemical records of three cores along a bathymetric transect (775‐, 1,359‐, and 1,908‐m water depths), at the transition between the Adriatic DW‐ formation area and the Eastern Mediterranean. In all three cores, sedimentation rates are distinctly higher during S1, corresponding with enhanced runoff emanating from the Adriatic hinterland. Hence, major runoff did not only come from southern but also from northern borderlands in this period. During sapropel formation, enhanced levels of primary productivity occurred in the surface waters and oxygen‐depleted conditions in the bottom waters for all sites. Conditions for sediment and bottom‐water below ~1.4 km water depth were sulfidic throughout S1, but for intermediate depth (775 m) were anoxic only during the first part (S1a). Bottom‐water oxygenation interrupted S1 formation at water depths down to ~1.4 km, during two brief episodes, at 8.2 and 7.4 cal. ka BP. From the 7.4 cal. ka BP ventilation onward, the transition to more oxygenated bottom‐water conditions was more progressive for the intermediate water depth site (775 m) than for the deeper sites. Conditions remained fully oxic for all water depths following the S1‐MarkerBed ventilation event. Possibly, the onset of continuously oxic conditions started slightly earlier at intermediate depth (775 m; 6.6 ± 0.3 cal. ka BP) than at greater depths (1,359 m, 1,908 m; 6.0 ± 0.3 cal. ka BP).