A large drilling campaign has been conducted across sediments of the Tertiary Molasse Basin and the underlying Mesozoic in Northern Switzerland in the context of underground disposal of radioactive waste. The ~300-400 m thick Mesozoic low-permeability rock sequence of interest is located between the regional aquifers made of Malm limestone at the top and dolomite/limestone formations of the Muschelkalk at the bottom. Locally, water-conducting zones occur in Dogger marl/limestone (Hauptrogenstein) below the Malm and/or in Keuper sandstone/dolomite above the Muschelkalk aquifer. Here we report on the distribution of the natural tracers δ²H and δ¹⁸O in porewater and groundwater from eight new boreholes in three study areas. The distribution of these tracers is the result of hydrogeological processes acting in the past, and their analysis offers unique possibilities to decode large-scale transport processes. The large data set allows us to compare the variability of δ¹⁸O and δ²H vertically as well as laterally in the three areas (∼20 km apart) and in the 2–4 boreholes in each area (a few km apart). The eight isotope profiles show many similarities, but also distinct features that are related to the lateral variation of aquifer properties, tectonic setting and topography, and the geometry of the aquifer-aquitard systems. Boundaries of the profiles are typically given by groundwater in the Malm (one location in the Dogger) and Muschelkalk aquifer, and locally by water-conducting zones in the Keuper. Maximum isotope values in the central part of the profiles plot to the right of the GMWL (Global Meteoric Water Line) to different degrees, as do values in the Malm aquifer. Towards the Keuper aquifer (if present) and the Muschelkalk aquifer, the values decrease smoothly and sharply, respectively, and approach the GMWL. The sharp decrease towards the Muschelkalk aquifer indicates a change in the isotope signature in the recent past or is related to low porosity and low diffusivity values in adjacent anhydrite layers. The two tracers δ²H and δ¹⁸O show different trends in the more central parts (almost constant or decreasing with depth, respectively). These differences are very likely inherited from pre-Pleistocene processes, i.e., before the present-day signatures in the aquifers came into play. Transport simulations are used to narrow down the timing of changes in the aquifer signatures in the more recent past (10 ka to few Ma ago). The data presented here demonstrate that (1) lateral variability is limited, even though the low-permeability zones are found at different depths, meaning that transport regimes were similar over large times of the past, (2) the known lateral variability of the Keuper aquifer is confirmed by the porewater profiles, (3) diffusion can explain the observed profile shapes and (4) signatures in the central parts of the low-permeability zone are oldest in the sense that they are furthest away from the GMWL.