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Study region: Albaida Valley, Spain. Study focus: Rivers are experiencing a rapid biodiversity loss largely due to water quality degradation imposed by anthropogenic activities. To show the capability of modeling to inform water management at watershed scales, this research develops an eco-hydrological model of the Albaida Valley (Spain). SWAT (Soil and Water Assessment Tool) is used for modeling of discharge and nutrients after calibration with SWAT-CUP (SWAT Calibration and Uncertainty Program). Results from SWAT are coupled to regressions between nutrients concentrations and macroinvertebrate-based metrics obtained from field monitoring. The spatio-temporal assessment of ecological status of streams is then carried out using simulated chemical and biological quality indicators (nitrate, ammonium, phosphorus, and macroinvertebrates). New hydrological insights for the region: Management measures (e.g., improving treatment of wastewater and/or adopting policies for reducing fertilizer use) are needed as the ecological status of Albaida Valley rivers is mostly classified as poor because of nutrients pollution. The reasonably low uncertainty in the model prediction (expressed by R-factor: discharge (0.2–0.61), nitrate (0.79–1.27) and total phosphorus (0.8–1.68)) demonstrates the potential of the presented model for future applications (i.e., for investigating possible responses of the Albaida Valley ecosystem to changes in climate, land-use, and local management policies). The modeling approach provided in this study could be generally used as a complementary technique to field monitoring in assessing and managing ecological conditions of rivers.