Understanding the wetting properties of chemically modified inorganic surfaces with random nanoscale topographies is of fundamental importance for diverse applications. This issue has hitherto continuously been the subject of considerable controversies. Herein, we report a thorough investigation of the wettability–topography–chemistry balance for a nanostructured surface with random topography, the main challenge being decoupling topography from surface chemistry. For this purpose, we use a superficially nanostructured aluminum substrate chemically modified by fatty acid monolayers. From atomic force microscopic data, we extract a variety of parameters describing the surface topography by means of variogram calculations, a method originally developed by geostatisticians to explore large surfaces. Moreover, by using log and power transforms, we establish a consistent relationship relating wettability, topography, and surface chemistry. Interestingly, we demonstrate that the water contact angle comprises a contribution due to the surface composition, originating from hydrophobization through alkyl chains, and a contribution due to the surface topography, particularly its stochastic feature. This model is valid in the Wenzel region; it provides guidelines for tuning the wetting properties of inorganic surfaces with random nanoscale topographies.