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By combining seismic and stratigraphic interpretations from both deep (hydrocarbon and geothermal) and shallow (groundwater) boreholes, this study enhances the quality of subsurface models in the relatively poorly understood middle-deep domain (200–1500 m depth). It presents new seismic interpretations of the Miocene strata of the Breda Subgroup and the Pliocene strata of the Oosterhout Formation, two key targets for geothermal energy and high-temperature heat storage, aiming to constrain the distribution and lateral thickness variations of these aquifers. The seismic interpretation study led to the development of updated base and top depth maps for the formations within both the Breda Subgroup and the Oosterhout Formation. Notably, the Groote Heide and Diessen Formations can now be interpreted further north into the Netherlands, beyond previous mapping efforts in the Achterhoek and Roer Valley Graben. This work provides a framework for future local-scale mapping and modelling of the Breda Subgroup and Oosterhout Formation. Additionally, the geothermal potential of the Breda Subgroup is assessed through petrophysical analysis and the generation of reservoir property maps, as porosity and permeability.