Various theories have been put forward regarding the salination mechanism in the Jordan-Dead Sea Rift Valley and its branching valleys. None of these have suggested current subsurface seawater penetration to the internally drained Judea Group aquifer, as a part of the system. The hydrogeological configuration is a combination of a low water table and a rather low groundwater divide, resulting in a shallow sea-fresh water interface. In most of the area the interface is expected to be situated above the base of the aquifer. As a result current seawater intrusion is possible across the ground water divide through the Yizre'el and Beersheva valleys which dissect Israel and connect the Mediterranean and the Jordan-Dead Sea Rift Valley. The model suggested herein is in accordance with, or cannot be rejected on the basis of the chemistry and isotope composition of the saline waters. In the highly flushed aquifers of the internal valleys, brackish water with marine affinity suggests current infiltration of seawater. This mechanism is additional to other sources, such as deep-seated highly-concentrated brines and entrapped fossil seawater, all of which are diluted by the flow of cyclic freshwaters.