The Sea of Galilee, located in the northern part of the Dead Sea rift, is currently an intermediate fresh-water lake. It is postulated that during a short highstand phase of former Lake Lisan in the late Pleistocene, saline water percolated into the subsurface. Since its recession from the Kinarot basin and the instantaneous formation of the fresh-water lake (the Sea of Galilee), the previously intruded brine has been flushed backward toward the lake. Numerical simulations solving the coupled equations of fluid flow and of solute and heat transport are applied to examine the feasibility of this hypothesis. A sensitivity analysis shows that the major parameters controlling basin hydrodynamics are lake-water salinity, aquifer permeability, and aquifer anisotropy. Results show that a highstand period of 3000 yr in Lake Lisan was sufficient for saline water to percolate deep into the subsurface. Because of different aquifer permeabilities on both sides of the rift, brine percolated into a aquifers on the western margin, whereas percolation was negligible on the eastern side. In the simulation, after the occupation of the basin by the Sea of Galilee, the invading saline water was leached backward by a topography-driven flow. It is suggested that the percolating brine on the western side reacted with limestone at depth to form epigenetic dolomite at elevated temperatures. Therefore, groundwater discharging along the western shores of the Sea of Galilee has a higher calcium to magnesium ratio than groundwater on the eastern side.