In geothermal reservoir systems, changes in pore pressure due to production (depletion), injection or temperature changes result in a displacement of the effective stresses acting on the rock matrix of the aquifer. To compensate for these intrinsic stress changes, the rock matrix is subjected to poroelastic deformation through changes in rock and pore volume. This in turn may induce changes in the effective pore network and thus in the hydraulic properties of the aquifer. Therefore, for the conception of precise reservoir models and for long-term simulations, stress sensitivity of porosity and permeability is required for parametrization. Stress sensitivity was measured in hydrostatic compression tests on 14 samples of rock cores stemming from two boreholes of the Upper Jurassic Malm aquifer of the Bavarian Molasse Basin. To account for the heterogeneity of this carbonate sequence, typical rock and facies types representing the productive zones within the thermal reservoir were used. Prior to hydrostatic investigations, the hydraulic (effective porosity, permeability) and geomechanical (rock strength, dynamic, and static moduli) parameters as well as the microstructure (pore and pore throat size) of each rock sample were studied for thorough sample characterization. Subsequently, the samples were tested in a triaxial test setup with effective stresses of up to 28 MPa (hydrostatic) to simulate in-situ stress conditions for depths up to 2000 m. It was shown that stress sensitivity of the porosity was comparably low, resulting in a relative reduction of 0.7–2.1% at maximum effective stress. In contrast, relative permeability losses were observed in the range of 17.3–56.7% compared to the initial permeability at low effective stresses. Stress sensitivity coefficients for porosity and permeability were derived for characterization of each sample and the different rock types. For the stress sensitivity of porosity, a negative correlation with rock strength and a positive correlation with initial porosity was observed. The stress sensitivity of permeability is probably controlled by more complex processes than that of porosity, where the latter is mainly controlled by the compressibility of the pore space. It may depend more on the compaction of precedented flow paths and the geometry of pores and pore throats controlling the connectivity within the rock matrix. In general, limestone samples showed a higher stress sensitivity than dolomitic limestone or dolostones, because dolomitization of the rock matrix may lead to an increasing stiffness of the rock. Furthermore, the stress sensitivity is related to the history of burial diagenesis, during which changes in the pore network (dissolution, precipitation, and replacement of minerals and cements) as well as compaction and microcrack formation may occur. This study, in addition to improving the quality of input parameters for hydraulic–mechanical modeling, shows that hydraulic properties in flow zones largely characterized by less stiff, porous limestones can deteriorate significantly with increasing effective stress.