In many grabens of the West European Rift System, several drilling projects are targeting fluid conductive faults to produce electricity with geothermal energy. In order to reach the adequate temperatures, the targeted faults are located in the basement rocks or at the basement/cover interface. Unfortunately, the basement rock facies and structural data useful for reservoir modelling are often poorly constrained because of the lack of boreholes deeper than 2000 m and seismic information on the deep subsurface. With the aim to outline the basement structure in the Upper Rhine Graben, two aeromagnetic surveys were conducted where the basement outcrops in the Northern Vosges, with different flight parameters and types of magnetometers. An interpolator using equivalent sources for gridding these two surveys is described by Gavazzi et al. (this issue). Here, we describe the geological interpretation of these surveys. We demonstrate the consistency between the total magnetic field intensity and the outcropping lithological units organized in ENE‐WSW subvertical bands. In detail, three main blocks were delineated, separated by N‐S faults linked to the graben formation and ENE‐WSW inherited Hercynian faults. The latter faults, together with more local NE‐SW and NW‐SE faults compartmentalize the N‐S oriented basement rocks. This is relevant for geothermal prospection where the N‐S faults are the main targets because fluid flow through other fault systems is deemed restricted. With a focus on the interface between the Northern Vosges and the Upper Rhine Graben, we also demonstrate considerable segmentation on the main graben boundary faults.