The internal geological structure of the Northeast German Basin (NEGB) is affected by intense salt diapirism and by the presence of several stratified aquifer complexes of regional relevance. The shallow Quaternary to late Tertiary freshwater aquifer is separated from the underlying Mesozoic saline aquifers by an embedded Tertiary clay enriched aquitard (Rupelian Aquitard). An important feature of this aquitard is that hydraulic connections between the upper and lower aquifers do exist in areas where the Rupelian Aquitard is missing (hydrogeological windows). Three-dimensional thermohaline numerical simulations are carried out to investigate the effects of such hydrogeological windows in the Rupelian Aquitard on the resulting groundwater, temperature, and salinity distributions. Numerical results suggest that hydrogeological windows act as preferential domains of hydraulic interconnectivity between the different aquifers at depth and enable vigorous heat and mass transport which causes a mixing of warm and saline groundwater with cold and less saline groundwater within both aquifers. In areas where the Rupelian Aquitard confines the Mesozoic aquifer, dissolved solutes from major salt structures are transported laterally giving rise to plumes of variable salinity content ranging from few hundreds of meters to several tens of kilometers. Furthermore, destabilizing thermal buoyancy forces may overwhelm counteracting stabilizing salinity induced forces offside of salt domes. This may result in buoyant upward groundwater flow transporting heat and mass to shallower levels within the same Mesozoic Aquifer.