Soil water storage and movement are highly heterogeneous across landscapes and their response to spatiotemporal variations in meteorological forcing is complex. While different pools of soil water (including bound and mobile water) are observed, the mechanisms of soil water movement in semi-arid and sub-humid regions are not well understood due to high variation in soil water storage conditions. The Taihang Mountain is a headwater region that recharges both groundwater and surface water systems of the North China Plain, where groundwater levels have been declining and water storage loss is serious. Increasing land cultivation in the Taihang Mountain areas has increased evapotranspiration and reduced both surface runoff and groundwater recharge. Although extreme precipitation is critical for groundwater recharge in the headwater regions, the response mechanism of soil water movement and groundwater recharge remains unclear. In this study, soil water movement and groundwater recharge mechanisms in a cultivated farmland (FL) and land under natural vegetation (NV) were determined for a normal and an extreme precipitation year through the combined use of soil water content and stable isotopes of water (18O and 2H). Soil water got enriched in δ18O and δ2H (δ18O changed from −11.2 to −7.0‰ at NV and from −11.1 to −4.4‰ at FL; δ2H changed from −71 to −49‰ at NV and from −73 to −30% at FL) with increasing soil depth during the growing season suggesting that winter precipitation was generally transported via advection dispersion flow mechanism. However, this process was accompanied by the mixing of previously enriched soil water after large rain events (20–50 mm/day) during the rainy season in a normal precipitation year. Water movement changed from translatory flow to preferential flow after extreme precipitation in a wet precipitation year. Cultivation intensified water evaporation in the top soil layer (upper 10–20 cm), and induced preferential flow down to 50 cm soil depth under FL relative to land under NV. Thus, cropping significantly reduced groundwater recharge. Excessive storm during a wet year produced bypass flow after the first rainstorm, which rapidly recharged deep soil layers (50–100 cm depth). Bypass flow induced by excessive precipitation and contributed the most to groundwater in FL. The observed rapid response of soil water and groundwater to extreme precipitation events is critical for soil and water management to mitigate problems such as nitrate leaching and groundwater contamination in headwater regions of semi-arid and sub-humid areas.