A deep core hole, drilled in the middle of the Dead Sea penetrated the Pleistocene-Holocene section, revealed an alternating sequence of fresh water and evaporitic (gypsum, halite) deposits. The vertical facies variations were interpreted as related mainly to lake level changes during this period. The present study, however, proposes an additional factor that influenced these changes, namely subsurface seawater intrusion from the Mediterranean Sea to the endorheic Dead Sea Basin. This proposed process is controlled by the elevation and head difference between both base levels at a given time, because the Mediterranean Sea level also fluctuated during the discussed period. We find that in times of smaller head differences, and assumed lower seawater intrusion, a gypsum facies prevailed in the Dead Sea Basin. In times of greater head differences and assumed more abundant seawater intrusion a halite facies prevailed because of greater sodium chloride input into the Dead Sea.