Knowledge of soil water dynamics in the deep vadose zone provides valuable information on the temporal and spatial variability of groundwater recharge. However, semi-arid climate can complicate how the input of water, such as irrigation, can contribute to potential groundwater recharge. This study assessed the recharge rates and their timing under irrigated cropland from a semi-arid region of northern Iran. A deep drainage (10 m) experiment was performed and in situ soil water content was measured to analyze the soil water dynamics and model hydraulic parameters using HYSDRUS-1D. The best parameters selected from inverse parameter optimization were used to calibrate model and estimate the long-term (20-year) average groundwater recharge and the influence of the root zone, unsaturated zone and the time scale on the recharge processes. The simulated annual flux ranged from 24 mm to 268 mm (mean of 110 mm) at 2-m depth and ranged between 26 mm to 207 mm (mean of 95 mm) at the 10-m depth. High fluxes, observed between December and April, may be the result of greater precipitation combined with the irrigation return flow. The May-October period showed a gradual decrease in flux at the depth of 2 m. At the depth of 10 m, the flux showed some continuity (base flux) during the long-term recharge simulation. In total, 12.7% of the input water contributed to the recharge of the groundwater. The annual soil water fluxes were almost similar irrespective of depth below the root zone and the flux rates did not show any clear relation between the different components of the water budget at any depth. This approach improved our understanding of the recharge process in the deep vadose zone in a semiarid region and can help for the development of effective management of groundwater resources.