It was suggested that brine of the Dead Sea rift has originated from a residual product of intensively evaporated seawater that invaded the rift, precipitated halite, and later interacted through dolomitization with the host rock during subsurface migration. Detection of this brine in many deep wells located at distances as far as 100 km away from the rift was attributed to long-distance migration of the brine. The physical feasibility of such migration, which probably spanned the past 3–6 m.y., is quantitatively tested and verified in this study by using paleohydrologic modeling. The structural formation of the rift is described by a chronological sequence of geologic cross sections serving as the basis for hydrodynamic calculations, which assess the effects of the structure on fluid migration, salinity redistribution, and heat transport across the sedimentary basin. Results indicate that two basin-scale ground-water systems, one atop the other but with opposite flow directions, coexisted in the Dead Sea rift valley. The first is a topography-driven flow of meteoric water from the surrounding highlands toward the rift through relatively shallow aquifers (≤ 1 km). The second is a density-driven migration of the Dead Sea brine through deep aquifers (4–5 km) in the opposite direction. The configuration of these flow systems has changed during the structural evolution of the Dead Sea rift, illustrating the interrelationships among basin formation, paleohydrology, and paleogeochemistry.