Groundwater recharge and capillary rise are key factors in water balance and management studies carried out in irrigated areas with shallow groundwater tables. In this study, the mathematical model SWAP-EPIC was applied to analyse the processes of groundwater recharge and capillary rise in the Hetao Irrigation District of the upper Yellow River basin. The model was calibrated and validated using non-weighing lysimeter data collected in 2007 and 2008, respectively. Simulations of soil water content, groundwater depth, leaf area index and yield fitted well with observations. The calibrated model was further used to analyse the response changes of groundwater recharge and capillary rise under different groundwater depth scenarios. Results indicated that capillary rise rate increased as crop roots developed, averaging 2.3 mm d−1during the mid-stage while groundwater was set at 100 cm depth. Groundwater contribution to crop growth was significant when the depth of the groundwater table was less than 150 cm, but was irrelevant for depths over 200 cm. Despite similar amounts of water being applied in each irrigation event, groundwater recharge varied significantly, resulting in recharge coefficients that varied from zero to 0.59. The amount of rainfall occurring previous to an irrigation event, lower evapotranspiration rates and shallower groundwater table depths resulted in higher antecedent soil moistures during an irrigation event and subsequently more effective groundwater recharge. The analysis of groundwater recharge and capillary rise processes will be useful in increasing field irrigation efficiency, improving the accuracy of groundwater modelling by reducing uncertainties, and making relevant management decisions in Hetao. Copyright © 2015 John Wiley & Sons, Ltd.