Recent geochemical and hydrological findings show that the water quality of the base flow of the Lower Jordan River, between the Sea of Galilee and the Dead Sea, is dependent upon the ratio between surface water flow and groundwater discharge. Using water quality data, mass-balance calculations, and actual flow-rate measurements, possible management scenarios for the Lower Jordan River and their potential affects on its salinity are investigated. The predicted scenarios reveal that implementation of some elements of the Israel–Jordan peace treaty will have negative effects on the Jordan River water salinity. It is predicted that removal of sewage effluents dumped into the river (∼13 MCM/a) will significantly reduce the river water’s flow and increase the relative proportion of the saline groundwater flux into the river. Under this scenario, the Cl content of the river at its southern point (Abdalla Bridge) will rise to almost 7000 mg/L during the summer. In contrast, removal of all the saline water (16.5 MCM/a) that is artificially discharged into the Lower Jordan River will significantly reduce its Cl concentration, to levels of 650–2600 and 3000–3500 mg/L in the northern and southern areas of the Lower Jordan River, respectively. However, because the removal of either the sewage effluents or the saline water will decrease the river’s discharge to a level that could potentially cause river desiccation during the summer months, other water sources must be allocated to preserve in-stream flow needs and hence the river’s ecosystem.