Holocene eastern Mediterranean Sea sediments contain an organic-rich sapropel S1 layer that was formed in oxygen-depleted waters. The spatial distribution of this layer revealed that during S1 deposition, deep waters were anoxic below a depth of 1800 m. However, whether this boundary permanently existed from the early to the mid-Holocene has not been examined yet. To answer this question, a multi-proxy approach was applied to a core retrieved close to the 1800 m boundary (at 1780 m). We measured the bulk sediment elemental composition, the stable isotopic composition of the planktonic foraminifer Globigerinoides ruber and the abundance of benthic foraminifera since the last deglaciation. The result indicates that authigenic U and Mo accumulation began around 13-12 cal ka BP, in concert with surface water freshening estimated from the G. ruber delta O-18 record. The onset of bottom and pore water oxygen depletion occurred prior to S1 deposition inferred from barium enrichment. In the middle of the S1 deposition period, reduced authigenic V, Fe and As contents and the Br/Cl ratio indicated short-term bottom-water re-oxygenation. A sharp Mn peak and maximal abundance for benthic foraminifera marked a total recovery for circulation at approximately 7 cal ka BP. Based on our results and existing data, we suggest that S1 formation within the upper 1780 m of the eastern Mediterranean Sea was preconditioned by reduced ventilation, resulting from excess freshwater inputs due to insolation changes under deglacial conditions that initiated between 15 and 12 cal ka BP within the upper 1780 m. Short-term re-oxygenation in the Levantine Basin is estimated to have affected bottom water at least as deep as 1780 m in response to cooling and/or the reduction of freshwater inputs. We tentatively propose that complete ventilation recovery at the S1 termination was depth-dependent, with earlier oxygenation within the upper 1780 m. Our results provide new constraints on vertical water column structure in the eastern Mediterranean Sea since the last deglaciation.