Abstract. Seismic methods are emerging as efficient tools for imaging the subsurface to investigate the weathering zone. The structure of the weathering zone can be identified by differing shear wave velocities as various weathering processes will alter the properties of rocks. Currently, 3D subsurface modelling of the weathering zone is gaining increasing importance as results allow the identification of the weathering imprint in the subsurface not only from top to bottom but also in three dimensions. We investigated the 3D weathering structure of monzogranite bedrock near the Pan de Azúcar National Park (Atacama Desert, northern Chile), where the weathering is weak due to the arid climate conditions. We set up an array measurement that records seismic ambient noise, which we used to extract the horizontal-to-vertical spectral ratio (HVSR) curves. The curves were then used to invert for 1D shear wave velocity (Vs) models, which we then used to compile a pseudo-3D model of the subsurface structure in our study area. To invert the 1D Vs model, we applied a transdimensional hierarchical Bayesian inversion scheme, allowing us to invert the HVSR curve with minimal prior information. The resulting 3D model allowed us to image the granite gradient from the surface down to ca. 50 m depth and confirmed the presence of dikes of mafic composition intruding the granite. We identified three main zones of fractured granite, altered granite, and the granite bedrock in addition to the mafic dikes with relatively higher Vs. The fractured granite layer was identified with Vs of 1.4 km s−1 at 30–40 m depth, while the granite bedrock was delineated with Vs of 2.5 km s−1 and a depth range between 10 and 50 m depth. We compared the resulting subsurface structure to other sites in the Chilean coastal cordillera located in various climatic conditions and found that the weathering depth and structure at a given location depend on a complex interaction between surface processes such as precipitation rate, tectonic uplift and fracturing, and erosion. Moreover, these local geological features such as the intrusion of mafic dikes can create significant spatial variations to the weathering structure and therefore emphasize the importance of 3D imaging of the weathering structure. The imaged structure of the subsurface in Pan de Azúcar provides the unique opportunity to image the heterogeneities of a rock preconditioned for weathering but one that has never experienced extensive weathering given the absence of precipitation.