Abstract Headwater catchments provide essential water and nutrients to downstream ecosystems. The timing and evolution of their transport is shaped in part by the ‘invisible’ subsurface structure but have been largely unexplored at the watershed scale. This raises a fundamental question: how and to what extent does subsurface structure influence streamflow and solute transport in montane watersheds? Here, we test controls of three‐dimensionally resolved subsurface structure on solute transport, which reflects source waters and water residence time. We integrate the geophysically mapped architecture of Coal Creek, a headwater catchment in the Colorado River Basin, into numerical flow‐transport models. Our results reveal greater vertical connectivity elongates flow paths and enhances deep groundwater contributions to streams, therefore substantially influencing the timing and magnitude of solute transport. In contrast, watershed‐integrated outlet discharge can be predicted without high‐resolution subsurface information. These findings demonstrate incorporating subsurface architecture is critical for predicting ecosystem health and contaminant transport.