The Molasse Basin is one of the most promising areas for deep geothermal exploitation in Germany and the target horizon is the aquifer in the Upper Jurassic carbonates. Carbonate deposits can be very heterogeneous even over a small area due to diagenetic processes and varying depositional environments. The preferential targets for geothermal exploitation in carbonate deposits are fault zones, reef facies and karstified areas, since they are expected to act as hydraulically permeable zones due to high porosity and high permeability. Therefore, identifying these structures and characterizing, e.g., their internal porosity distribution are of high importance. This can be accomplished using 3D reflection seismic data. Besides structural information, 3D seismic surveys provide important reservoir properties, such as acoustic impedance, from which a porosity model can be derived. In our study area in Munich we carried out a seismic amplitude inversion to get an acoustic impedance model of the Upper Jurassic carbonate reservoir using a 3D seismic data set, a corresponding structural geological model, and logging data from six wells at the ‘Schäftlarnstraße’ geothermal site. The impedance model and porosity logs were than used to calculate a porosity model. The model shows a wide porosity range from 0 to 20% for the entire reservoir zone and the lithology along the wells reveals that dolomitic limestone has the highest porosities and calcareous dolomite has the lowest porosities. The study area is cut by a large W–E striking fault, the Munich Fault, and the footwall north of it shows higher porosities and more intense karstification than the hanging wall to the south. Considering the entire study area, an increase in porosity from east to west is observed. Furthermore, we identified a complex porosity distribution in reef buildups and pinnacle reefs. The reef cores have mostly low porosities of, e.g., < 3% and the highest porosities of up to 7 to 14% are observed at the reef caps and on the reef slopes. The reef slopes show a characteristic interfingering of the reef facies with the surrounding bedded facies, which indicates a syn-sedimentary reef development with slightly varying build up growth rates. We also assessed the reservoir quality with regard to porosity distribution and determined areas with moderate to good quality for geothermal exploitation by defining porosity evaluation levels. The porosity evaluation maps show that the carbonate rocks of Berriasian to Malm $$\zeta$$
ζ
1 are preferential targets for exploitation, especially in the footwall of the Munich Fault and to the west of the hanging wall, because these areas are characterized by high porosities due to intense karstification of bedded and massive facies, although the latter is mainly restricted to reef caps and reef slopes.