Natural fractures are ubiquitous in crustal rocks and often dominate the bulk properties of geological formations. The development of numerical tools to model the geometry, geomechanics and fluid flow behaviour of natural fracture networks is a challenging issue which is relevant to many rock engineering applications. The thesis first presents a study of the statistics and tectonism of a multiscale fracture system in limestone, from which the complexity of natural fractures is illustrated with respect to hierarchical topologies and underlying mechanisms. To simulate the geomechanical behaviour of rock masses embedded with natural fractures, the finite-discrete element method (FEMDEM) is integrated with a joint constitutive model (JCM) to solve the solid mechanics problems of such intricate discontinuity systems explicitly represented by discrete fracture network (DFN) models. This computational formulation can calculate the stress/strain fields of the rock matrix, capture the mechanical interactions of discrete rock blocks, characterise the non-linear deformation of rough fractures and mimic the propagation of new cracks driven by stress concentrations. The developed simulation tool is used to derive the aperture distribution of various fracture networks under different geomechanical conditions, based on which the stress-dependent fluid flow is further analysed. A novel upscaling approach to fracture network models is developed to evaluate the scaling of the equivalent permeability of fractured rocks under in-situ stresses. The combined JCM-FEMDEM model is further applied to simulate the progressive rock mass failure around an underground excavation in a crystalline rock with pre-existing discontinuities. The scope of this thesis covers the scenarios of both two-dimensional (2D) and three-dimensional (3D) fracture networks with pre-existing natural fractures and stress-induced new cracks. The research findings demonstrate the importance of integrating explicit DFN representations and conducting geomechanical computations for more meaningful assessments of the hydromechanical behaviour of naturally fractured rocks.