The Jordan Valley is a heavily modified, data-limited transboundary river basin where water availability is constrained by both climate conditions and intensive human intervention. This study applies an integrated hydrological and hydrogeochemical modeling framework using the Soil and Water Assessment Tool (SWAT) to quantify basin-scale water availability and quality and to assess climate change impacts for the period 2000–2021. Results indicate that the basin is strongly evapotranspiration-dominated, with mean annual precipitation of 298.9 mm and precipitation-derived evapotranspiration accounting for 66.3% of rainfall. When externally supplied irrigation water is included, total evapotranspiration increases markedly, highlighting the strong dependence of agriculture on imported surface water and groundwater abstractions. Only a small fraction of total water input contributes to river discharge toward the Dead Sea, indicating a very limited internal water surplus. Hydrological dynamics are largely controlled by upstream dams and transboundary diversions, while nitrate and sediment simulations demonstrate a close coupling between hydrology, land use, and water quality. Climate projections suggest further reductions in water availability during the 21st century, exacerbating existing water scarcity. Overall, the study illustrates how intensive regulation and irrigation dependency constrain water availability in the Jordan Valley and in similar heavily modified transboundary river basins.