The Callovian-Oxfordian (COx) clayey unit is being studied in the Eastern part of the Paris Basin at depths between 400 and 500 m depth to assess of its suitability for nuclear waste disposal. The present study combines new mineralogical and isotopic data to describe the sedimentary history of the COx unit. Petrologic study provided evidence of the following diagenetic mineral sequence: (1) framboidal pyrite and micritic calcite, (2) iron-rich euhedral carbonates (ankerite, sideroplesite) and glauconite (3) limpid calcite and dolomite and celestite infilling residual porosity in bioclasts and cracks, (4) chalcedony, (5) quartz/calcite. Pyrite in bioturbations shows a wide range of δ34S (−38‰ to +34.5‰), providing evidence of bacterial sulphate reduction processes in changing sedimentation conditions. The most negative values (−38‰ to −22‰), measured in the lower part of the COx unit indicate precipitation of pyrite in a marine environment with a continuous sulphate supply. The most positive pyrite δ34S values (−14‰ up to +34.5‰) in the upper part of the COx unit indicate pyrite precipitation in a closed system. Celestite δ34S values reflect the last evolutionary stage of the system when bacterial activity ended; however its deposition cannot be possible without sulphate supply due to carbonate bioclast dissolution. The 87Sr/86Sr ratio of celestite (0.706872-0.707040) is consistent with deposition from Jurassic marine-derived waters. Carbon and oxygen isotopic compositions of bulk calcite and dolomite are consistent with marine carbonates. Siderite, only present in the maximum clay zone, has chemical composition and δ18O consistent with a marine environment. Its δ13C is however lower than those of marine carbonates, suggesting a contribution of 13C-depleted carbon from degradation of organic matter. δ18O values of diagenetic chalcedony range between +27‰ and +31‰, suggesting precipitation from marine-derived pore waters. Late calcite crosscutting a vein filled with chalcedony and celestite, and late euhedral quartz in a limestone from the top of the formation have lower δ18O values (not, vert, similar+19‰), suggesting that they precipitated from meteoric fluids, isotopically close to present-day pore waters of the formation. Finally, the study illustrates the transition from very active, biotic diagenesis to abiotic diagenesis. This transition appears to be driven by compaction of the sediment, which inhibited movement of bacterial cells by reduction of porosity and pore sizes, rather than a lack of inorganic carbon or sulphates.