The effects of weathering on the mineralogical and petrophysical properties of the western Uganda Archaean crystalline basement were investigated using outcrop samples. This study aimed to characterize a typical composite vertical weathering profile by the integration of data from samples with variable degree of alteration, ranging from fresh to completely weathered. A detailed description of samples is proposed, using different observation methods (e.g., x-ray computed tomography scanning and quantitative evaluation of minerals by scanning electron microscopy analysis system). Petrophysical analyses were carried out to fully describe the porous network of the samples (e.g., mercury porosimetry [φ] and permeability [k] measurements). A geometric factor reported in the literature is also used to describe the variable complexity of the porous network through the weathering profile. This multimethod study revealed two distinct domains in the weathering profile, separated by a sharp property transition. The lower part of the profile is characterized by dominant planar pore structures and represents a high transfer zone for fluid circulation (φ ≤ 8%–10%; k ≤ 500 md). The upper part of the profile is characterized by high clay content and dominant vacuole-shaped matrix porosity. This represents a high fluid storage zone (φ ≈ 30%; k ≤ 1 d). Both parts are locally preserved from complete clay plugging by hydrodynamic drainage, resulting from a long-term geomorphic evolution. In the case of preservation of such a composite weathering profile after basement burial in a sedimentary basin with hydrocarbon potential, these domains may represent a significant area for petroleum exploration. Properties described in this study indicate that the weathered basement in such a basin can act as a large reservoir for hydrocarbons or as a favorable migration zone at the interface between the basement and the sedimentary cover. Finally, several proxies are proposed to help for the recognition of these two domains from cutting analyses and well logging.