We present a high‐resolution study covering the past 19 ka from the southeastern Mediterranean Sea, based on benthic foraminiferal faunas and their stable oxygen and carbon isotopes. These data are integrated with previously published and newly acquired planktic foraminiferal data from the same sediment core in order to investigate the benthic‐planktic coupling and its response to past suborbital climate variability. On a millennial timescale, foraminiferal communities and their isotopic signatures vary following three main time periods (late glacial, sapropel S1 [~10.1–6.5 ka], and mid‐Holocene to Late Holocene). Within these intervals, we identified short‐timescale changes related to the carbon export and hydrological conditions. During the deglaciation, and except for the Younger Dryas, the coupled benthic‐planktic data indicate an overall poorly mixed water column with a low productivity. During S1 event, our data confirm the presence of a highly stratified water column, with enhanced primary productivity export to the deep sea, being associated to high Nile River activity. While the foraminiferal ecosystem is strongly driven by the combined influence of overturning circulation and the Nile River activity until the end of the African humid period, we suggest a more regional eastern Mediterranean climatic‐driven response of the foraminiferal community over the mid‐Holocene to Late Holocene. A strong multicentennial variability, probably associated to solar forcing, was found for both benthic and planktic records, and a supplementary 1,600‐year mode was found for the benthic data, suggesting a potential overturning circulation‐driven forcing for the latter.