Vegetation plays an active role in soil water dynamics and water balance in atmosphere-soil-vegetation-groundwater system. Therefore, we characterised soil water transportation at depths of 0-4.0 m, induced by root water uptake of groundwater-dependent Salix across a whole growth stage, as well as taking place in non-vegetated soil, in the semi-arid Ordos basin of China. The results show that: soil moisture content showed clear heterogeneity under the combined influence of evaporation, rainfall and root water uptake. Thus, the soil profile was divided into the climate impacted layer, the transitional layer, and groundwater supporting layer. Root water uptake increased the variability of soil water in the vadose zone and changed the classification structure. The impacts of different rainfall regimes on soil moisture and vegetation response at the individual plant scale were systematically analysed. The rainwater infiltration hysteresis as connected to rainfall intensity, soil depth and the roots-system preferential channel were confirmed, as was the canopy-shading effect. Further, an exponential-logarithmic normal composite root water uptake distribution was obtained, via an inverse method. Of the accumulated 356.3 precipitation in 2016, the annual soil water increase was 97.9 mm for bare site, increased by 10.2% in total, accounting for 25.5% of the precipitation of that year. Conversely, for vegetated site, annual soil water decrease registered at 254.40 mm, decreased by 28.3% in total. The contrastive experiment indicates that root water uptake processes change the soil water flow field and aggravate water scarcity, resulting in soil desiccation in the deep local soil layers and groundwater depletion. The dried soil layers blocked water interchange, which is extremely detrimental to ecohydrological processes. Our results provide a scientific basis within which the hydrodynamic processes of vegetation in semi-arid regions may better be understood and inspire research to find a balance between groundwater management and vegetation replanting.