The influence of in-situ stresses on flow processes in fractured rock is investigated using a novel modelling approach. The combined finite-discrete element method (FEMDEM) is used to model the deformation of a fractured rock mass. The fracture wall displacements and aperture changes are modelled in response to uniaxial and biaxial stress states. The resultant changes in flow properties of the rock mass are investigated using the Complex Systems Modelling Platform (CSMP++). CSMP++ is used to model single-phase flow through fractures with variable aperture and a permeable rock matrix. The study is based on a geological outcrop mapping of a low density fracture pattern that includes the realism of intersections, bends and segmented features. By applying far-field (boundary) stresses to a square region, geologically important phenomena are modelled including fracture-dependent stress heterogeneity, the re-activation of pre-existing fractures (i.e. opening, closing and shearing), the propagation of new fractures and the development of fault zones. Flow anisotropy is investigated under various applied stresses and matrix permeabilities. In-situ stress conditions that encourage a closing of fractures together with a more pervasive matrix-dominated flow are identified. These are compared with conditions supporting more localised flow where fractures are prone to dilatational shearing and can be more easily exploited by fluids. The natural fracture geometries modelled in this work are not perfectly straight, promoting fracture segments that dilate as they shear. We have demonstrated the introduction of several realistic processes that have an influence on natural systems: fractures can propagate with wing cracks; there is the potential for new fractures to connect with existing fractures, thus increasing the connectivity and flow; blocks can rotate when bounded by fractures, bent fractures lead to locally different aperture development; highly heterogeneous stress distributions emerge naturally. Results presented in this work provide a mechanically rigorous demonstration that a change in the stress state can cause reactivation of pre-existing fractures and channelling of flow in critically stressed fractures.