High purity fluorite veins (acid grade > 97 % CaF2) are generally rare in a global context. The fluorite-(±quartz-calcite) veins in the Aukam Valley mining district in SW Namibia have not previously been studied but due to their excellent exposure they are an ideal natural laboratory to study such mineralization. These veins cross-cut Mesoproterozoic high-grade gneisses and granites (Namaqua-Natal Metamorphic Province) close to the unconformity with the overlying late-Neoproterozoic Nama Group sedimentary rock cover. Based on the regional context, their genesis has been assumed to be related to nearby fluorite-bearing pegmatites. However, the present contribution provides new microthermometry data from vein fluorite (with 25.0–25.6 wt% NaCl and Th of 270–300 °C) that indicate precipitation from a mixed fluid with two chemically contrasting end-members for the early paragenetic fluorite stage. However, it was not possible to identify the chemical composition of the endmembers. Based on the chemical composition of the fluid mixture and the regional geological context, we propose that these end-members are F-rich brines sourced from the Namaqua basement and Ca-rich limestone-derived formation fluids of the Nama Group. A fluorite-overgrowing quartz precipitation is likely the effect of post-mixing fluid cooling as the fluid inclusions hosted in quartz show lower homogenization temperatures (Th 230–260 °C) with similar salinity. Locally, late-stage calcite is recognized with fluid inclusion compositions (0.2–2.7 wt% NaCl and Th of 60–92 °C) different from those observed in the fluorite and quartz. With significantly lower homogenization temperatures, they likely represent precipitates formed during the shutdown and collapse of the hydrothermal system. The fluorite veins are hosted in post-Cambrian N-trending brittle structures that probably formed during the opening of the South Atlantic in late Mesozoic times. Interestingly, similar massive fluorite mineralization on both sides of the Atlantic Ocean is also likely associated with Pangea rifting and known from numerous mining districts operating on unconformity-related hydrothermal veins in Central and North America, northern Africa and Europe.