Abstract The Calcaires du Barrois Formation is a succession of dominantly micritic limestone of Kimmeridgian to Tithonian age, outcropping in the eastern part of the Paris Basin. This is an active karstic aquifer of interest to Andra (French National Agency for Radioactive Waste Management), who are studying the feasibility of a deep geological repository of radioactive waste in an underground research laboratory located approximately 450 m below the surface. Surface installations of the Industrial Centre for Geological Disposal project are planned in the upstream recharge zone of the aquifer. It is of primary interest to characterize the Calcaires du Barrois Formation to provide guidelines for the planning and sizing of these facilities, to minimize the impact on the aquifer system. An integrated study was designed for this purpose, linking petrography (thin section and scanning electron microscopy), carbon and oxygen stable isotope geochemistry, X-ray diffraction, petrophysics and geomechanics. It is based on the analysis of three key cored wells penetrating the formation at different relative depths. The Calcaires du Barrois have undergone several stages of diagenesis that have defined the current properties. Unconformities associated with the Jurassic–Cretaceous transition led to prolonged early subaerial exposures during which freshwater flowed efficiently through the upper half of the formation. Through mineralogical stabilization, among other processes, microporosity was preserved in micrites in this interval consisting of clean limestone with thin marl layers. The lower half of the formation, more argillaceous, was not or was only slightly affected by this early meteoric diagenesis, and recrystallization and cementation of micrites occurred during burial diagenesis, involving chemical compaction. Later, during the return to the surface associated to the Cenozoic orogens, another phase of meteoric diagenesis affected the uppermost few metres below the outcropping portions of the formation, but without modifying significantly the previously acquired petrophysical properties. Consequently, an intra-formational boundary was progressively developed at around 75 m (from the top reference). This boundary separates (1) a lower half of the Calcaires du Barrois with dense and tight micrites, showing high Young's modulus values, and a moderate intensity of fractures, from (2) an upper half with microporous micrites showing low Young's modulus values, and almost devoid of fractures. A transitional zone of about 30 m thick, with intermediate properties, sitting above this boundary and below the only thin metre-scale macroporous grainstone level of the formation, accommodated most of the deformation linked to the Cenozoic Western European orogens and is intensively fractured. The current hydrogeological model considers a purely sedimentological boundary to delimit two sub-aquifers within the Calcaires du Barrois Formation. This will have to be reappraised since it is here demonstrated that the real boundary is located significantly higher in the formation and is inherited from a multi-stage diagenetic history. These findings will complement and influence planning for the Industrial Centre's project.