The Jurassic clay-rich aquitard sequence underlying the Swiss Molasse Basin is locally penetrated by unusually frequent veins consisting of calcite ± celestite, in particular in the Schlattingen-1 and Oftringen drill cores. The veins are linked to extensional brittle structures, with shear senses ranging between dip-slip and strike-slip. Deformation triggered transient and localised events of fluid flow within the aquitard followed by sealing of the structures by the vein minerals. Vein calcite was dated by LA-ICP-MS analysis using the U/Pb method. While this was a demanding undertaking, given the low U and high common Pb contents of calcite, 9 significant ages could be obtained. Two groups of ages can be distinguished, namely 31–39 and 11–18 Ma. Both age groups are consistent with the known regional tectonic evolution. The older age group corresponds to the main phase of rifting in the Upper Rhine Graben, a major crustal discontinuity, whose effects were not limited to the graben proper but affected large parts of the Molasse Basin. The younger age group is linked to crustal tilting and related extensional deformation. Isotopic compositions of O and C in vein calcite from the Schlattingen-1 core show substantial variability but do not discriminate between veins of the two age groups. In contrast, 87Sr/86Sr ratios in veins show different signatures. The depth trend of 87Sr/86Sr ratios in veins fits well with that in pore water obtained by rock squeezing. The two data sets define a trend of values increasing with depth, connecting the current values in the embedding Malm and Keuper aquifer waters. This trend is best explained as a near-steady-state diffusion profile. While advective mixing of waters originating from the embedding aquifers to produce the veins, implying structures that cross cut the whole low-permeability sequence, cannot be discarded on the basis of existing data, it is considered more likely that the veins have local fluid sources. These are mixtures of local pore water with a possible contribution of water from the nearest aquifer, implying maximum vertical advection distances in the order of 50–100 m.