Lake Kinneret (LK), located within the Dead Sea Rift valley, is influenced by saline groundwater discharge and upward diffusion of solutes from deep sediments. The chemical composition and geological settings of these deep brines have not been comprehensively characterized. We present high-resolution porewater chemical profiles and analyses of major ion ratios to reconstruct the origin and evolutionary history of deep saline sources beneath LK. Concentrations of sodium, chloride, bromide and magnesium increase linearly with depth. The vertical gradients indicate an upward diffusive flux from a deep brine reservoir. In addition, Na/Cl, Br/Cl, and Mg/Cl molar ratios in LK porewaters deviate significantly from seawater evaporation trends and instead align with brine evolution pathways characteristic of the Dead Sea Rift system. These Ca-chloride brines originated from interactions between evaporated seawater and carbonate rocks during late Neogene marine incursions into the northern rift valleys and Dead Sea basin. The ion ratios in porewater of LK show the same ion ratios trend in Dead Sea porewater dated to approximately 29–26 ka BP. These values correspond closely with those documented for Last Glacial Lake Lisan (LGLL), the hypersaline lake that preceded the modern Dead Sea, providing evidence that Lisan waters intruded into the Kinneret basin during Marine Isotope Stage 2. Na/Cl, Br/Cl, and Mg/Cl ratios provide an independent confirmation of this connection. Our findings reveal that Lake Kinneret's salt sources are derived from trapped LGLL brine that represents an independent salinity source with management implications for Israel's major freshwater reservoir.