Organic‐rich layers (sapropels), preserved in eastern Mediterranean marine sediment records, represent pronounced perturbations to thermohaline circulation and environmental conditions in the basin, in response to enhanced African monsoon activity and subsequent massive freshwater discharge. During the most recent event, Sapropel S1 formed between 10.8 and 6.1 ka, when freshwater‐driven stratification caused seafloor anoxia below ~1,800‐m depth, as a result of both failure of deep water formation and enhanced productivity. Here we analyze coccolith assemblages from the open eastern Mediterranean that form a west‐east transect across the basin and provide insights on past environmental changes. We focus on holococcoliths, which are specifically produced by coccolithophores as part of their life cycle during the haploid phase. Since holococcolith calcification is characterized by nanocrystals highly susceptible to dissolution, we are testing their potential preservation under different bottom environmental conditions, including the effect of postdepositional oxidation. A comparison with benthic foraminifera assemblages in a core recovered close to Lybia reveals that holococcolith preservation is enhanced during seafloor reventilation and benthic foraminiferal repopulation in the middle to upper part of the record, before the actual sapropel termination. There are two such events of improved deep‐water oxygenation in the Aegean and Adriatic Seas at 8.2 and 7.4 ka. The latter episode marks the onset of the transition to restored circulation in the eastern Mediterranean Sea, due to resumption of deep‐water formation in the southern Aegean Sea and the conclusion of enhanced biogenic productivity.