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In times of population growth, climate change, and increasing water scarcity around the world, it is important to take an objective look at water, a fundamental resource for life. Hydrodynamic modeling makes possible the research of different aspects of the water cycle and the evaluation of different hydrological and hydrogeological forecasting scenarios in the short and medium terms. The present research offers a more detailed scope at the hydrodynamic processes and their space-time distributions on a UE pilot in the Júcar River Basin, providing a calibrated and validated hydrodynamic model of 121 km river reach for 45 years period (1974–2019) on a daily scale. The obtained information is about discharge and water depths along the Júcar River reach within the hydrogeological boundaries of the Mancha Oriental Aquifer (MOA). The river–aquifer interactions have been represented as dynamic boundary conditions expressed as a difference between observed discharges measured in 3 gauging stations. The obtained calibration error performance evaluations of observed and simulated values cover two periods, according to observed data availability from gauging station 08036 with resulting R2 for both discharges and water depths over 0.96. The model validation results were obtained for a different gauge 08132 and the determination coefficients R2 also perform very well with value of 0.90. The model developed might be useful for decision making in water resources management and can be used to generate simulated time series of water depths, levels, discharges, and velocities in reaches where gauging measurements are not available with a desired space-time resolution (from meter/second to kilometer/month). Estimation of critical discharge value (1.973 m3s−1) for system equilibrium, based on the balance between losing and gaining sub-reaches of the river, is also made with a statistical significance at 95% for hydrologic years 2007–2010, period influenced by restrictions in groundwater withdrawals. The results of the present research are important for the proper and objective management of the scarce water resources on a watershed scale in Júcar River Basin, a complex case study representing semiarid climate, growing anthropogenic pressures, and complex river–aquifer interactions. The used approach of dynamic representation of the river–aquifer interactions as distributed source boundary condition in the one-dimensional hydrodynamic model might be applied in another study case on similar scale.