A vadose zone flow and transport model for Los Alamos Canyon is presented that demonstrates that a comprehensive understanding of vadose zone hydrologic processes can be obtained by integrating data from geologic, hydrologic, and site characterization sources. The complex hydrostratigraphy of the canyon is captured using geologic characterization of extensive deep-well drilling samples, along with surface mapping. A water budget study for the surface and shallow subsurface hydrology is used to estimate spatially varying infiltration rates along the canyon. Three-dimensional flow model results show that mesa-top infiltration rates on the order of 1 mm yr−1, and canyon-bottom rates several orders of magnitude higher, capture the water content profiles from available wells within the model domain. However, a range of a factor of three higher and lower than these mean values is also consistent with the data. Transient flow simulations show that episodic infiltration events can be effectively averaged in steady-state flow modeling, but transients that last on the order of a decade or more, such as climate related or anthropogenically induced transients, significantly change the predicted water content. Modeling of tritium transport through the vadose zone indicates that even for a nonsorbing contaminant, most, but not all, of the contaminant released since in the past 40 yr should still be present in the vadose zone. The mass predicted to reach the water table is primarily in locations in the canyon where the Bandelier Tuff is not present. Available groundwater surveillance data for regional aquifer water are consistent with this result.