Hydrologic modeling has been a useful approach for analyzing water partitioning in catchment systems. It will play an essential role in studying the responses of watersheds under projected climate changes. Numerous studies have shown it is critical to include subsurface heterogeneity in the hydrologic modeling to correctly simulate various water fluxes and processes in the hydrologic system. In this study, we test the idea of incorporating geophysics-obtained subsurface critical zone (CZ) structures in the hydrologic modeling of a mountainous headwater catchment. The CZ structure is extracted from a three-dimensional seismic velocity model developed from a series of two-dimensional velocity sections inverted from seismic travel time measurements. Comparing different subsurface models shows that geophysics-informed hydrologic modeling better fits the field observations, including streamflow discharge and soil moisture measurements. The results also show that this new hydrologic modeling approach could quantify many key hydrologic fluxes in the catchment, including streamflow, deep infiltration, and subsurface water storage. Estimations of these fluxes from numerical simulations generally have low uncertainties and are consistent with estimations from other methods. In particular, it is straightforward to calculate many hydraulic fluxes or states that may not be measured directly in the field or separated from field observations. Examples include quickflow/subsurface lateral flow, soil/rock moisture, and deep infiltration. Thus, this study provides a useful approach for studying the hydraulic fluxes and processes in the deep subsurface (e.g., weathered bedrock), which needs to be better represented in many earth system models.