Abstract In high‐mountain watersheds, the critical zone holds crucial life‐sustaining water stores in the form of shallow groundwater aquifers. To better understand the role that the critical zone plays in moderating hydrologic response to fluxes at the surface and in the subsurface, the hydrologic properties must be characterized over large scales (i.e., that of the watershed). In this study, we estimate porosity from geophysical measurements across a 58‐ha area to depths of ~80 m. Our observations include velocities from seismic refraction, downhole nuclear magnetic resonance logs, downhole sonic logs, and samples acquired by push coring. We use a petrophysical approach by combining two rock physics models, a porous medium for the saprolite and a differential effective medium for the fractured rock, into a Bayesian inversion. The inverted geophysical porosities show a positive correlation with measured values ( R 2 = 0.93). We extrapolate the porosity estimates from 30 individual seismic refraction lines to a 3D volume below our study area using ordinary kriging to quantify the water holding capacity of our study area. Our results reveal that the critical zone in our study area holds ~2.9 × 10 6 ± 9.6 × 10 5 m 3 of water, where 34% of this storage is in the saprolite, 55% is in the fractured rock, and the remaining 11% is in the bedrock.