Meteoric fresh groundwater from shallow aquifers and hot brines from deep aquifers mix while emerging from several springs along the western coast of the Sea of Galilee, a freshwater lake located within the Dead Sea Rift Valley, Israel. After the rainy season, when elevations of the groundwater table rise in the regional aquifers and discharge rates of springs increase, solute concentrations decrease at Tabha springs but, surprisingly, increase at Fulya springs, apparently suggesting two different salinization mechanisms. Two detailed geologic cross sections were constructed, one across the rift valley at Tabha and a second at Fulya, each about 6 km deep and 70 km long. The hydrodynamics in these cross sections were analyzed using a two-dimensional finite element code that solves the coupled variable-density groundwater flow and heat transfer equations. Numerical simulations indicate that a topography-driven flow model explains both spring systems, and the opposite salinity behavior results from the different hydrogeological configurations of the two subsurface drainage basins. At Fulya, both aquifers, the shallow one and the deeper one, are partially phreatic, whereas at Tabha, the deeper aquifer is totally confined. The response of springs to changes in elevation of groundwater table were simulated, reproducing field observations. This analysis has implications for the management scheme for the lake and its surrounding aquifers.