© Author(s) 2015. Clarifying the variations of groundwater recharge response to a changing non-stationary hydrological process is important for efficiently managing groundwater resources, particularly in regions with limited precipitation that face the risk of water shortage. However, the rate of aquifer recharge is difficult to evaluate in terms of large annual-variations and frequency of flood events. In our research, we attempt to simulate related groundwater recharge processes under variable climate conditions using the SWAT Model, and validate the groundwater recharge using the Hydrus Model. The results show that annual average groundwater recharge comprised approximately 33 % of total precipitation, however, larger variation was found for groundwater recharge and surface runoff compared to evapotranspiration, which fluctuated with annual precipitation variations. The annual variation of groundwater resources is shown to be related to precipitation. In spatial variations, the upstream is the main surface water discharge area; the middle and downstream areas are the main groundwater recharge areas. Validation by the Hydrus Model shows that the estimated and simulated groundwater levels are consistent in our research area. The groundwater level shows a quick response to the groundwater recharge rate. The rainfall intensity had a great impact on the changes of the groundwater level. Consequently, it was estimated that large spatial and temporal variation of the groundwater recharge rate would be affected by precipitation uncertainty in future.