Disposal of nuclear waste in deep geological formations is expected to induce thermal fluxes for hundreds of years with maximum temperature reaching about 100–150 °C in the nearfield argillaceous environment. The long-term behavior of clays subjected to such thermal gradients needs to be perfectly understood in safety assessment considerations. In this respect, a Toarcian argillaceous unit thermally disturbed by the intrusion of a 1.1-m wide basaltic dike at the Perthus pass (Herault, France), was studied in detail as a natural analogue. The thermal imprint induced by the dike was evaluated by a mineralogical, chemical and K–Ar study of the <2 μm clay fraction of shale samples collected at increasing distance from the basalt. The data suggest that the mineral composition of the shales was not significantly disturbed when the temperature was below 100–150 °C. Closer to the dike at 150–300 °C, changes such as progressive dissolution of chlorite and kaolinite, increased content of the mixed layers illite–smectite with more illite layers, complete decalcification and subsequent increased content of quartz, were found. At the eastern contact with the dike, the mineral and chemical compositions of both the shales and the basalt suggest water–rock interactions subsequent to the intrusion with precipitation of palagonite and renewed but discrete deposition of carbonate. A pencil cleavage developed in the shales during the dike emplacement probably favored water circulation along the contact. Strontium isotopic data suggest that the fluids of probable meteoric origin, reacted with Bathonian and Bajocian limestones before entering the underlying Toarcian shales. By analogy with deep geological radioactive waste repositories, the results report discrete mineralogical variations of the clays when subjected to temperatures of 100–150 °C that are expected in deep storage conditions. Beyond 150 °C, significant mineralogical changes may alter the physical and chemical properties of the shales, especially of the clay fraction. Also, the development of structural discontinuities in the so-called thermally disturbed zone might be of importance as these discontinuities might become zones for preferential fluid circulation. Finally, the study emphasizes the use of Rb–Sr and K–Ar isotopic systems as tracers of local circulating fluids related to low-grade thermal imprints.