The chemical composition of groundwater in the Jordan Valley, along the section between the Sea of Galilee and the Dead Sea, is investigated in order to evaluate the origin of the groundwater resources and, in particular, to elucidate the role of deep brines on the chemical composition of the regional groundwater resources in the Jordan Valley. Samples were collected from shallow groundwater in research boreholes on two sites in the northern and southern parts of the Jordan Valley, adjacent to the Jordan River. Data is also compiled from previous published studies. Geochemical data (e.g., Br/Cl, Na/Cl and SO₄/Cl ratios) and B, O, Sr and S isotopic compositions are used to define groundwater groups, to map their distribution in the Jordan valley, and to evaluate their origin. The combined geochemical tools enabled the delineation of three major sources of solutes that differentially affect the quality of groundwater in the Jordan Valley: (1) flow and mixing with hypersaline brines with high Br/Cl (>2 × 10⁻³) and low Na/Cl (<0.8) ratios; (2) dissolution of highly soluble salts (e.g., halite, gypsum) in the host sediments resulting in typically lower Br/Cl signal (<2 × 10⁻³); and (3) recharge of anthropogenic effluents, primarily derived from evaporated agricultural return flow that has interacted (e.g., base-exchange reactions) with the overlying soil. It is shown that shallow saline groundwaters influenced by brine mixing exhibit a north–south variation in their Br/Cl and Na/Cl ratios. This chemical trend was observed also in hypersaline brines in the Jordan valley, which suggests a local mixing process between the water bodies.