Many of the great Phanerozoic salt basins share a common paleogeography, in which a deep lake or sea is separated from the ocean by a narrow barrier. Examples include the Aptian evaporites of the South Atlantic rift basins and the Messinian salt deposits of the Mediterranean Sea and the North Caspian depression. Marine transgressions over the barrier have been proposed as the origin for saline conditions in these basins. We test an alternate hypothesis, that subsurface seepage of seawater through the barrier was a significant source of water, influencing both water level and water composition. Our model permits flux of water and salt into and out of the basin via (1) seepage through the barrier; (2) evaporation from the water surface; (3) rainfall and/or rivers; and (4) incorporation into basin sediments. Our investigation focuses on three settings, a modern analog in the Gregory Rift of northern Kenya, the Messinian Mediterranean basin, and the Early Cretaceous Aptian salt basins of the South Atlantic. We test our model through a numerical simulation, applying reasonable values for the dimensions of the barrier, differences in water level, and hydraulic conductivities to calculate flow rates through the barrier. Modeling results indicate that flux of seawater through a barrier to a peripheral basin ranges from the dominant component of lake water to insignificant, depending on the climate, size of the peripheral basin, and hydraulic conductivity of the barrier. The flux of salt is significant over the full range of modeled hydraulic conductivities, producing brines in the peripheral lake and/or sea within 0.5 m.y. in most cases. This demonstrates that seepage through the barrier can account for lithologic and organic geochemical evidence for saline water conditions, and that marine transgressions across the barrier are not necessary to explain the apparent high salinities.