For the successful realization and productivity prediction of new hydrothermal projects in the South German Molasse Basin, the hydraulic matrix properties of the Upper Jurassic Malm reservoir have to be determined as accurately as possible. To obtain specific information on the distribution of the petrophysical parameters (e.g., rock density, porosity, and permeability) 363 samples of rare drilling cores from the reservoir northeast of Munich (wells Moosburg SC4 and Dingolfing FB) were investigated using different experimental methods. Additionally, porosity was calculated by a downhole resistivity log of a nearby borehole close to Munich for comparison and the attempt of transferability of the data set to other locations within the Central Molasse Basin. Core data were divided into groups of different stratigraphic and petrographic units to cover the heterogeneity of the carbonate aquifer and provide data ranges to improve reservoir and prediction models. Data for effective porosity show a high variance from 0.3 to 19.2% throughout this heterogeneous aquifer. Permeability measured on core samples is scattered over several orders of magnitude (10 −4-10 2 mD). Permeability models based on the porosity-permeability relationship were used to estimate permeability for the whole aquifer section and identify possible flow zones. A newly developed empirical model based on distinct lithofacies types allows a permeability estimation with a deviation < 10 mD. However, fractured, karstified, and vuggy zones occurring in this typically karstified, fractured, and porous reservoir cannot yet be taken into account by the model and result in an underestimation of permeability on reservoir scale. Overall, the dominant permeability trends can be mapped well using this model. For the regional transfer and the correlation of the results, a core-related porosity/ permeability log for the reservoir was compiled for a well close to Munich showing similarities to the core investigations. The validation of the regional transferability of the parameter set to other locations in the Molasse Basin was carried out by correlation with the interpreted log data of a well near Munich.