Oxygen Minimum Zones (OMZs) are expanding in modern oceans due to anthropogenically-driven climate and environmental change. In the Eastern Mediterranean Sea (EMS), OMZs developed in the early Holocene as a result of decreased intermediate water ventilation, increasing temperature, and increased Nile discharge and primary productivity. Here, we report benthic foraminiferal numbers (BFN) and species abundances, together with redox-sensitive trace metals (RSTM), and iron and phosphorus speciation from two sediment cores sampled at intermediate depths (1200 and 1430 m) from the SE Levantine shelf. The main aim of our study is to better understand the sequence of redox changes during sapropel S1 deposition caused by biogeochemical processes affecting the sapropel intermediate water mass. The use of benthic foraminifera indices (diversity and oxygen) together with iron speciation and RSTM (V, Mo and U) enables detailed description of the changing oxygen/redox status of the overlying water. Prior to sapropel S1 deposition at ∼10.2 ka BP, RSTM suggest that the overlying water was well oxygenated, but benthic foraminifera numbers (BFN) suggest that oxygen levels had already begun to decrease. There was then a pulse of increased export carbon from the enlarged Nile flood plume, as shown by increased BFN at the beginning of sapropel S1. Shortly after, RSTM and Fe-S systematics suggest that the water column transitioned from dysoxic to anoxic, non-sulfidic. Anoxic conditions then persisted at 1200 m depth, but RSTM and benthic foraminifera indices suggest that deeper waters at 1430 m were more likely dysoxic, until the 8.2 ka BP global cooling event. The benthic foraminifera and inorganic redox proxies then suggest a second period of anoxic, non-sulfidic conditions, with a gradual return to well ventilated waters at the end of sapropel deposition at ∼6 ka BP. There was enhanced burial of authigenic P throughout sapropel deposition, derived from the deposition and subsequent release of organic-P and iron bound-P during diagenesis. Phosphorus recycling from the sediment and in the overlying water column added reactive P to these mid-depth waters, a process which has the potential to result in a positive feedback in systems where such waters are upwelled into the photic zone. The past EMS thus represents a template which can be used to predict biogeochemical changes in settings that evolve towards anoxic, non sulfidic conditions, which may occur in some areas as modern climate and environment change causes the continued expansion of modern OMZs and hypoxic areas adjacent to modern major rivers.