Abstract. Changing stress regimes control fracture network geometry and influence porosity and permeability in carbonate reservoirs. Using outcrop data analysis and a displacement-based linear elastic finite-element method, we investigate the impact of stress regime change on fracture network permeability. The model is based on fracture networks, specifically fracture substructures. The Latemar, predominantly affected by subsidence deformation and Alpine compression, is taken as an outcrop analogue for an isolated (Mesozoic) carbonate buildup with fracture-dominated permeability. We apply a novel strategy involving two compressive boundary loading conditions constrained by the study area's NW–SE and N–S stress directions. Stress-dependent heterogeneous apertures and effective permeability were computed in the 2D domain by (i) using the local stress state within the fracture substructure and (ii) running a single-phase flow analysis considering the fracture apertures in each fracture substructure. Our results show that the impact of the modelled far-field stresses at (i) subsidence deformation from the NW–SE and (ii) Alpine deformation from N–S increased the overall fracture aperture and permeability. In each case, increasing permeability is associated with open fractures parallel to the orientation of the loading stages and with fracture densities. The anisotropy of permeability is increased by the density and connectedness of the fracture network and affected by shear dilation. The two far-field stresses simultaneously acting within the selected fracture substructure at a different magnitude and orientation do not necessarily cancel each other out in the mechanical deformation modelling. These stresses affect the overall aperture and permeability distributions and the flow patterns. These effects – potentially ignored in simpler stress-dependent permeability – can result in significant inaccuracies in permeability estimation.