Carbon‐rich layers exist at both sides of the Mediterranean Sea sedimentary record and are called sapropels and organic rich layers (ORLs), respectively in the eastern and western basins. They have different levels of organic carbon accumulation and seafloor oxygen deprivation. The most recent sapropel and ORL depositions have a different timing, approximately 10.8‐6.1 and 14.5‐9.0 ka respectively. Here we investigate oxygen isotopic records of three foraminifera species that occupy different habitats within the Sicily Channel water column since ~ 12.0 ka, thus in the sill between the eastern and western Mediterranean basins. These data are ice volume‐corrected, to get information on water masses density variability, and are accompanied by benthic foraminifera δ13C measurements to establish Sicily Channel seafloor ventilation. Our results, and the comparison with other chronologically well‐constrained Mediterranean records, highlight the connection of the two sub‐basins due to monsoon activity. The end of the maximum Nile River flooding at ~ 9.2 ka, and eastern Mediterranean seafloor reventilation above 1800‐1500 m depth at ~ 8.2 and 7.2 ka, left a clear signature in the intermediate water isotopic record of the Sicily Channel. Concurrently, the western Mediterranean deep water circulation experienced a significant recovery after a long period of slowdown. We argue that African monsoon weakening was transmitted into the western Mediterranean, through the intermediate layer of circulation, where deep water formation took place and brought oxygen to the seafloor.