Vegetation plays an active role in soil water dynamics and water balance in groundwater-soil-plant-atmosphere continuum systems. Therefore, we characterized soil water transport at depths of 0–4.0 m induced by root water uptake (RWU) at a groundwater-dependent Salix site during the whole growth stage and compared the results with those from a non-vegetated soil site, in the semiarid Ordos basin of China. The results showed that: during the whole experimental period, evapotranspiration at the vegetated site was more than twice evaporation at the bare site, indicating that the transpiration exceeded the evaporation and was the main output of soil water. For the bare site, the increase of soil water storage in the lysimeter was 97.9 mm in total, accounting for 27.5% of the precipitation, with 16.8% of rainfall as retention in the shallow vadose zone and 10.7% of rainfall as seepage below 150 cm depth. Conversely, in the vegetated site, rainfall-driven soil water was mainly consumed by vegetation, and the decrease of soil water storage was 254.4 mm in total, with no seepage being observed. Although the root system as the preferred channel improved the soil infiltration capacity, it did not mean that the deep soil water recharge increased. The infiltrated rainfwater could not offset the water consumption of the root system. An exponential normal composite RWU model obtained by the reverse method showed that the water deficit soil layers caused by RWU changed the soil water flow field and blocked soil water interchange. Consequently, deep soil water and groundwater could not be replenished by precipitation. Our results emphasize ascertaining the hydrodynamic processes of vegetation in semiarid regions and help to strike a balance between vegetation restoration and groundwater management.