Salinization in coastal aquifers is a global phenomenon resulting from the overexploitation of scarce water resources. The Gaza Strip is one of the most severe cases of salinization, as accelerated degradation of the water quality endangers the present and future water supply for over 1 million people. We investigate the chemical and isotopic (87Sr/86Sr, δ11B, δ18O, δ2H, and δ34SSO4) compositions of groundwater from the southern Mediterranean coastal aquifer (Israel) and the Gaza Strip in order to elucidate the origin of salinity and boron contamination. The original salinity in the eastern part of the aquifer is derived from discharge of saline groundwater from the adjacent Avedat aquitard (Na/Cl 1, high B/Cl, SO4/Cl, and HCO3, 87Sr/86Sr ~ 0.7083; δ11B ~ 48?), although the δ18O-δ2H slope is identical to that of the Avedat aquitard. The geochemical data suggest that dissolution of pedogenic carbonate and gypsum minerals in the overlying loessial sequence generated the Ca-rich solution that triggered base exchange reactions and produced Na- and B-rich groundwater. The geochemical data show that most of the salinization process in the Gaza Strip is derived from the lateral flow of the Na-rich saline groundwater, superimposed with seawater intrusion and anthropogenic nitrate pollution. The methodology of identification of multiple salinity sources can be used to establish a long-term management plan for the Gaza Strip and can also be implemented to understand complex salinization processes in other similarly stressed coastal aquifers.