Understanding the critical zone processes related to groundwater flows relies on underground structure knowledge and its associated parameters. We propose a methodology to draw the patterns of the underground critical zone at the catchment scale from seismic refraction data. The designed patterns define the structure for a physically based distributed hydrological model applied to a mountainous catchment. In that goal, we acquired 10 seismic profiles covering the different geomorphology zones of the studied catchment. We develop a methodology to analyze the geostatistical characteristics of the seismic data and interpolate them over the whole catchment. The applied geostatistical model considers the scale variability of the underground structures observed from the seismic data analysis. We use compressional seismic wave velocity thresholds to identify the depth of the regolith and saprolite bottom interfaces. Assuming that such porous compartments host the main part of the active aquifer, their patterns are embedded in a distributed hydrological model. We examine the sensitivity of classical hydrological data (piezometric heads) and geophysical data (magnetic resonance soundings) to the applied velocity thresholds used to define the regolith and saprolite boundaries. Different sets of hydrogeological parameters are used in order to distinguish general trends or specificities related to the choice of the parameter values. The application of the methodology to an actual catchment illustrates the interest of seismic refraction to constrain the structure of the critical zone underground compartments. The sensitivity tests highlight the complementarity of the analyzed hydrogeophysical data sets.