Ocean deoxygenation is a rising threat to marine ecosystems and food resources under present climate warming conditions. Organic-rich sapropel layers deposited in the Mediterranean Sea provide a natural laboratory to study the processes that have controlled the changes in seawater oxygen levels in the recent geological past. Our study is based on three sediment cores spanning the last 10 thousand years (10 kyr BP) and located on a bathymetric transect offshore the western distributaries of the Nile delta. These cores are partly to continuously laminated in the sections recording sapropel S1, which is indicative of bottom-water anoxia above the western Nile deep-sea fan. We used a combination of microfacies analyses and inorganic and organic geochemical measurements to reconstruct changes in oxygenation conditions at seasonal to millennial time-scales. The regular alternations of detrital, biogenic and chemogenic sublayers in the laminated sequences are interpreted in terms of seasonal changes. Our microfacies analyses reveal distinct summer floods and subsequent plankton blooms preceding the deposition of inorganic carbonates formed in the water-column during spring-early summer. The isotopic signature of these carbonates suggests year-round anoxic to euxinic bottom waters resulting in high levels of anaerobic remineralisation of organic matter and highlights their potential to reconstruct seawater chemistry at times when benthic fauna was absent. Synchronous changes in terrigenous input, primary productivity and past oxygenation dynamics on millennial time-scales obtained by our multi-proxy study show that runoff-driven eutrophication played a central role in driving rapid changes in oxygenation state of the entire Levantine Basin. Rapid fluctuations of oxygenation conditions in the upper 700 m water depth occurred above the Nile deep-sea fan between 10 and 6.5 ka BP while deeper cores recorded more stable anoxic conditions. These findings are further supported by other regional records and reveal time-transgressive changes in oxygenation state driven by rapid changes in primary productivity during a period of long-term deep-water stagnation.