Highly saline lithium-rich hydrothermal fluids (measured chloride concentration up to 44 g kg−1, lithium concentration up to 162 mg kg−1) occur in the deep calcareous Muschelkalk aquifer beneath the northern Alpine foreland (Molasse) basin. We have combined geologic, hydraulic, hydrochemical, and stress field data of the Triassic Muschelkalk aquifer beneath younger sediments of Triassic–Jurassic successions and the Cenozoic Molasse basin of SW-Germany for a synthesis to constrain the origin and development of these brines. In contrast to the regional southeast plunge of Jurassic and Cenozoic strata, low-gradient groundwater flow in the Upper Muschelkalk aquifer is to the north, induced by regional recharge from west, south, and east. The investigated area is seismically active and north trending maximum horizontal stress likely fosters development of necessary fracture permeability for northward flow in the competent carbonates of the Upper Muschelkalk aquifer. The highest lithium concentrations and total dissolved solids (TDS) can be found in the southern parts of the Muschelkalk aquifer. Here, the Muschelkalk Group overlays directly a crystalline basement swell separating two ENE-trending Permocarboniferous troughs. We argue that the highly saline lithium-rich fluids originate from fluid–rock interaction of meteoric water with Variscan crystalline basement rocks and entered the Muschelkalk aquifer on top of the basement swell by permeable faults and fractures. The marginal calcareous sand-rich facies of the Muschelkalk enables the inflow of brines from crystalline basement faults and fractures into the aquifer. We thus argue for an external origin of these brines into the aquifer and further intra-reservoir development by dilution with meteoric water.