The analysis of tracer profiles of porewaters is a valuable tool to understand transport processes in argillaceous rocks and to unravel the paleo-hydrogeology of a site. In this contribution, anionic tracers (Cl, Br) from eight boreholes located in three study areas (∼20 km apart) penetrating the ∼800 m thick Mesozoic sequence in northern Switzerland, were analysed. A specific focus was on the Opalinus Clay, a ∼100 m thick homogeneous claystone formation, foreseen as host rock for radioactive waste disposal in Switzerland, as well as its mostly clay-rich confining units. Using porewater extraction methods, such as high-pressure squeezing, advective displacement and aqueous extraction, a unique dataset of spatially highly resolved Cl and Br profiles could be obtained. These show systematic and comparable patterns suggesting common paleo-hydrogeological evolution paths for all three study areas. The scatter in the tracer profiles based on the aqueous extraction data are mostly related to the uncertainty in the estimation of the anion-accessible porosity fraction on one hand and in the water content data in the case of low-porosity calcareous rocks on the other. Differences between the study areas are in line with differences in aquifer characteristics. The current shape of the anion profiles is dominated by diffusive exchange with the bounding aquifers over the last several ten thousands to millions of years, as supported by numerical modelling. The Br/Cl signals also suggest the preservation of older signals related to halite dissolution and highly evolved evaporitic porewaters occurring in evaporite-bearing units of the Triassic. Overall, the adopted methodology has enabled to obtain a unique dataset of anionic tracers at regional scale providing a solid basis for understanding the regional paleo-hydrogeology of siting areas for a potential nuclear waste repository.