The flow rate of the Lower Jordan River has changed dramatically during the second half of the 20th century. The diversion of its major natural sources reduced its flow rate and led to drying events during the drought years of 2000 and 2001. Under these conditions of low flow rates, the potential influence of external sources on the river discharge and chemical composition became significant. Our measurements show that the concentrations of chloride, calcium, and sodium in the river water decrease along the first 20-km section, while sulfate and magnesium concentrations increase. These variations were addressed by a recent geochemical study, suggesting that ground water inflow plays a major role. To further examine the role of ground water, we applied mass-balance calculations, using detailed flow rate measurements, water samplings, and chemical analyses along the northern (upstream) part of the river. Our flow-rate measurements showed that the river base-flow during 2000 and 2001 was 500 to 1100 L s(-1), which is about 40 times lower than the historical flow rates. Our measurements and calculations indicate that ground water input was 20 to 80% of the river water flow, and 20 to 50% of its solute mass flow. This study independently identifies the composition of possible end-members. These end-members contain high sulfate concentration and have similar chemical characteristics as were found in agricultural drains and in the "saline" Yarmouk River. Future regional development plans that include the river flow rate and chemistry should consider the interactions between the river and its shallow ground water system.