A hydrogeologic conceptualization is critical to understand, manage, protect, and sustain groundwater resources, especially in regions where data are sparse, and accessibility is difficult. We used airborne electromagnetic (AEM), shallow seismic reflection and refraction data, and downhole nuclear magnetic resonance (NMR) logs to improve our understanding of an arid groundwater system influenced by palaeovalleys. In the current hydrogeologic conceptualization it is unknown if the palaeovalley and underlying bedrock aquifers are connected. We focused on defining the spatial distribution of saprolite, which is the layer of chemically altered rock separating the palaeovalley and bedrock aquifers. The AEM data provided an estimate of the top of saprolite but failed to effectively image the bottom. In contrast, the seismic data provided an estimate of the bottom of saprolite but failed to image the top. This unique geophysical combination of electrical and elastic data allowed us to map saprolite thickness in detail along a 1.7 km long transect that runs perpendicular the main trunk of a well-defined palaeovalley. We show that the palaeovalley is lined with a heterogenous layer of saprolite (3-120 m thick) that is thickest near the palaeovalley edges. Despite the variability, only a small percentage of the bedrock aquifer (8-17%) is in contact with the palaeovalley aquifer. Furthermore, the lack of an elastic boundary at the top of saprolite suggests that the porosity of the saprolite is similar to the palaeovalley sediments. An observation that is supported by the downhole NMR water contents. The electrical change at the top of saprolite is caused by a change in pore structure associated with the difference of weathering in situ versus transported materials. Our geophysical data suggest that the saprolite acts as an aquitard limiting groundwater exchange between the palaeovalley and bedrock aquifers.