For large-scale CO₂ and hydrogen storage, heterogeneous fractured media continue to pose a significant challenge for the accurate prediction of fluid transport and storage capacity. Under geomechanical perturbations such as induced seismicity or pressure evolution, the flow capacity and long-term integrity of storage sites are directly affected by these phenomena. [1]. Deformation-induced heterogeneity introduces significant uncertainty in predictive models [2], although emerging evidence indicates that seismicity does not inherently lead to fault leakage that compromises CO₂ storage [3]. In this work, a unified framework for stress-responsive transport in deep saline aquifers is developed by coupling transient pressure dynamics with fracture mechanics. High-fidelity simulations of heterogeneous rough fractures were performed to investigate the influence of fracture rugosity, orientation, and stochastic correlation fields. Six representative test cases spanning realistic ranges of fracture geometries and stress conditions were analyzed. Results indicate that the calculated equivalent permeability can vary from 1.4 to 18 times the values predicted by planar fracture approximations with averaged aperture [4], highlighting the critical impact of fracture heterogeneity on transport predictions. These findings provide improved guidance for evaluating fluid flow and solute migration in fractured aquifers, with direct implications for the safety and efficiency of CO₂ and hydrogen storage.