The residual dark unit of the most recent eastern Mediterranean sapropel (S1) is usually overlain by sediments with enhanced concentrations of MnOx in two separated layers. The variability and magnitude of the Mn enrichment at different locations and water depths indicate that Mn must have been added preferentially to sediments at intermediate (1–2 km) water depths. We propose a two-stage mechanism for the Mn enrichment that involves decreasing oxygenation with increasing water depth. This mechanism involves the loss of reduced Mn2+ from the deepest sediments (>2 km water depth) into overlying anoxic waters and a variable gain of MnOx in sediments in contact with oxygenated waters at shallower depth. In the S1 unit that receives the extra MnOx input, an upper higher Mn-enriched zone (>3 wt %) is maintained continuously at the top of the accumulating S1 unit because the pore waters are anoxic at shallow sediment depth while bottom waters are oxic to some degree. In a reactive-transport model, the Mn enrichment in the upper zone could not be supported by normal sediment diagenesis. Thus the MnOx in the upper Mn horizon must have formed mainly in the water column. The MnOx in the upper Mn-enriched zone adsorbed Mo and Li from seawater in a similar manner as other Mn-enriched oxic sediments, nodules, and crusts, with a Mn:Mo ratio of ∼600:1, a Mn:Li ratio of ∼750:1, and a δ98/95MoMOMO of −2.5 ‰.