Dual continuum computational models that include both porous media and discrete fracture zones are valuable tools in assessing groundwater flow and pathways in fractured rock systems. Fracture generation models can produce realisations of discrete fracture networks that honour geological structures and fracture propagation behaviours. A methodology and algorithm are presented to incorporate a discrete, complex and irregular fracture zone network, represented as a triangulated two-dimensional mesh, within an orthogonal three-dimensional finite-element mesh. Orthogonal fracture faces, between adjacent finite-element blocks, were used to represent the irregular discrete-fracture zone network. A detailed coupled density-dependent groundwater flow analysis of a hypothetical 104 km2 portion of the Canadian Shield has been conducted using the discrete-fracture dual continuum finite-element model FRAC3DVS-OPG to investigate the importance of large-scale fracture zone networks on flow and transport. Surface water features and a Digital Elevation Model (DEM) were applied in a GIS framework to delineate the sub-watershed and to populate the finite-element mesh. The crystalline rock between the structural discontinuities was assigned properties characteristic of those reported for the Canadian Shield. Total Dissolved Solids (TDS) concentrations of 300 g/l are encountered at depth. A comparison is made to a model which represents the fracture zones as an Equivalent Porous Medium (EPM). Differences in freshwater heads, TDS, and pore water velocities in fracture zones are demonstrated. The discrete fracture zone approach yields simulated TDS values which are lower at depth than TDS values simulated using the EPM approach, primarily due to higher simulated pore water velocities within the discrete fracture zones. Solute transport is sensitive to fracture zone characterisation and dispersivity values required to achieve stable solutions. Steady-state density-independent simulations using both approaches yield similar freshwater heads.