We quantify the 3D temperature distribution for a large and structurally complex intra-continental basin based on physical principles and considering a realistic approximation of the sedimentary fill as well as of the underlying crust and lithospheric mantle. Comparing observed temperatures with temperatures predicted by a 3D conductive, steady- state thermal model for the Central European Basin System (CEBS) we find a thick layer of mobilized Zechstein salt causes significant local temperature variations due to its high thermal conductivity compared to less conductive surrounding clastic sediments. This local pattern is superposed by a regional component originating in the deeper lithosphere.