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To address the issues of water shortages and the loss of agricultural products at harvest in northern Afghanistan, the Soil and Water Assessment Tool (SWAT) was applied for agricultural water resource management by simulating surface runoff in the Balkhab River basin (BRB) on a monthly basis from 2013 to 2018. Elevation, slope, land cover data, soil maps, and climate data such as temperature, precipitation, relative humidity, wind speed, and solar radiation were used as inputs in the SWAT modelling. During the dry season from July to September, the water resources downstream were basically attributed to baseflow from groundwater. In the calibration, the groundwater baseflow was estimated by analyzing station-recorded discharges for 190 springs. With the estimated baseflow, the SWAT results were markedly improved, with R² values of 0.70, 0.86, 0.67, and 0.80, Nash-Sutcliff efficiency (NSE) values of 0.52, 0.83, 0.40, and 0.57, and percent bias (PBIAS) values of 23.4, −8.5, 23.4, and 17.5 in the four different subbasins. In the validation, the statistics also indicated satisfactory results. The output of this study can be used in agricultural water resource management with irrigation practices and further in the assessment of climate change effects on the water resources in the BRB.