The spatial and temporal changes of the pore water along an argillaceous formation were studied on the basis of the chemistries of the fluids collected through the system. The study is based on chemical characterisation results of the pore water, which requires careful sampling and 4 years monitoring. The concept was applied to the water sampled from several boreholes drilled through the Opalinus Clay formation in the anticline at Mont Terri, Canton Jura, Switzerland. Asymmetrical gradients from the clay formation toward the limestone overburden are observed. In this upper formation, recharge with low mineralised water has caused the diffusion of species from the saline pore waters in the clay formation and their depletion. These species form concentration profiles from the underlying Jurensis Marl formation containing hydrophobic organic material toward the upper Lower Dogger Limestone formation. Non-sorbing species such as chlorides, bromides, iodides and sulphates as well as Na as a weakly sorbing cation form increasing concentration profiles from the Lower Dogger Limestone into the Opalinus Clay formation. Heavy water isotopes display similar profiles. The pH increases slightly downward through the system (from about 7 to 8) together with the total organic C (TOC) concentration, while the total inorganic C (TIC) concentration decreases from the Lower Dogger Limestone through the Opalinus Clay formation. A similar profile is observed for pe which decreases from the limestone groundwater (+2.5) toward the underlying marl water (−2.5). The water composition is discussed taking into account in-situ pore water dilution from recharge water by mean of a diffusion mechanism. Quantification of this transport process and of the consequent concentration profile is carried out through the 165 m thick Opalinus Clay layer, which was impregnated by fossil pore water derived from Tethys Ocean, considering a diffusion process that started about 10 Ma ago. The apparent diffusion coefficients estimated in the Opalinus Clay for Cl−, Br−, I– and Na+, on one hand, and, for 2H and 18O on the other are 2.6±0.8 and 5.2±1.5·10−11 m2 s−1, respectively. These values are compared with data gained from other argillaceous systems. The Opalinus Clay formation is likely to have acted as a geological nanoporous barrier for 10 Ma.