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Sustainable heat extraction is of utmost importance for the economic life of geothermal production systems. Especially in hydrothermal sedimentary basins, a temperature decrease at the production well prompts a financial loss. A premature thermal breakthrough occurred in one of the geothermal projects in the Greater Munich Area, a well-known region for deep, low enthalpy geothermal development in the Upper Jurassic carbonate reservoir (syn. Malm) beneath the North Alpine Foreland Basin. Accordingly, questions are raised regarding the geologic controls on the reservoir´s permeability, the occurring type of heat and mass transport mechanism, and the fitting reservoir model type. 3D seismic data interpretation delineates seismic scale structures potentially influencing the reservoir permeability. Geophysical borehole data characterize sub-seismic scale elements (fractures, karst, and lithofacies), where we correlate them with the inflow zones and the interpreted seismic scale structures. The integration of both scales delineates the reservoir heterogeneity controlled by a lateral change in the carbonate lithofacies overprinted by faults and fractures. A NNW-SSE oriented seismic scale structure matches the orientation of hydraulically active sub-seismic scale fractures, where they are aligned with the maximum horizontal stress orientation. This structure induces additional anisotropic permeability, providing a preferential hydraulic pathway between the wells of the project. This study recommends considering fractured reservoir models to simulate the mass and heat flow in the highly heterogeneous Malm carbonates instead of composite reservoir models of equivalent hydraulic properties. Finally, we present a hydrogeological model describing the reservoir's structural and matrix permeability distribution to act as a basic concept for future thermal-hydraulic numerical modeling. The applied methods in this study are applicable in similar geothermal systems with adequate seismic and geophysical borehole data for future geothermal reservoir characterization, modeling, and management.