Watershed hydrological processes controlled by subsurface structures that have hierarchical organization across scales, but there is a lack in multiscale model validation. In this study, using a comprehensive dataset collected in the forested Shale Hills catchment, we tested the series HYDRUS codes (i.e., HYDRUS-1D at the pedon scale, HYDRUS-2D at the hillslope scale, and HYDRUS-3D at the catchment scale) that included a hierarchical multi-dimensional modeling approach for water flow simulation in the vadose zone. There is good agreement between 1D simulations and measurements of soil moisture profiles controlled by soil hydraulic parameters and precipitation characteristics; however, short-term fluctuations in preferential flow were poorly captured. Notably, 2D and 3D simulations (Nash–Sutcliffe efficiency, ), which accounting subsurface preferential flow controlled by slope positions and shallow fractured bedrock, provided better results than 1D simulations (). Our modeling approach also illustrated that the studied watershed was characterized by weathered and un-weathered fracture bedrocks, which routed water through a network of subsurface preferential flow pathways to the first-order stream. Furthermore, a dual-porosity or anisotropy model produced more accurate predictions than a single-porosity or isotropy model due to a more realistic representation of local soil characteristics and layered structure. Our multi-dimensional modeling approaches credited with diagnosing and presenting the dominant hydrological processes and the interactions within soil-landscape features across one sloped catchment.