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Abstract Headwater catchments play a vital role in regional water supply and ecohydrology, and a quantitative understanding of the hydrological partitioning in these catchments is critically needed, particularly under a changing climate. Recent studies have highlighted the importance of subsurface critical zone (CZ) structure in modulating the partitioning of precipitation in mountainous catchments; however, few existing studies have explicitly taken into account the 3D subsurface CZ structure. In this study, we designed realistic synthetic catchment models based on seismic velocity‐estimated 3D subsurface CZ structures. Integrated hydrologic modeling is then used to study the effects of the shape of the weathered bedrock and the associated storage capacity on various hydrologic fluxes and storages in mountainous headwater catchments. Numerical results show that the weathered bedrock affects not only the magnitude but also the peak time of both streamflow and subsurface dynamic storage.