<p>Assessing surface and subsurface water resources in the Padsan River Watershed is crucial for sustainable agricultural water management and food security. This study aims to contribute to addressing sustainability challenges and regional food security concerns by assessing the spatiotemporal dynamics of river discharge and groundwater recharge within the watershed overlaying the River Irrigation Systems. The Soil and Water Assessment Tool (SWAT) Model, with bias-corrected Climate Hazards Group InfraRed Precipitation with Station Data (CHIRPS) to simulate watershed hydrology, simulated the watershed hydrology with strong performance metrics indicated by the strong Coefficient of Determination (<i>R</i>^<i>2</i>) and Nash-Sutcliffe efficiency (NSE) values. This demonstrated the good agreement between the simulated and observed river discharge. Results show that the annual river discharge is 595.20&#xa0;m³/s, and the yearly groundwater recharge rate is 427.18&#xa0;mm. These values were calculated based on the watershed spatiotemporal distribution, which provides more efficient estimates than conventional discrete measurements. Notably, agricultural areas exhibited the lowest groundwater recharge rates, emphasizing a vulnerability that could affect crop yields and regional food security while posing a threat with land subsidence and overexploitation. These findings underscore the need to incorporate groundwater recharge insights into irrigation system planning and water resource management by government entities and support the integration of groundwater recharge in the watershed’s Integrated Water Resources Management. Addressing low recharge rates is essential for enhancing sustainability and mitigating potential impacts on agricultural productivity. The results offer reliable estimates, serving as a crucial foundation for developing comprehensive strategies to design and plan water resource infrastructure.</p>