A three-dimensional numerical analysis of a 5734 km2 watershed situated in the Canadian Shield has been conducted to illustrate aspects of regional-scale groundwater flow in a crystalline rock setting. An essential requirement of the analysis is the preservation and accurate description of the complex topography, surface water drainage network, groundwater salinity distribution, and permeability distributions. The postglacial evolution of the groundwater flow system was investigated using the finite difference model SWIFT-III. Robustness was assessed by exploring the sensitivity of groundwater flow to topography, variable matrix permeability distribution models, pore-water salinity, and the dissipation of elevated initial pore pressures that result from ice that overlaid the watershed in the last glacial period. Groundwater flow analyses indicate that freshwater heads in all model layers are highly correlated with the complex surface topography such that the transition from zones of groundwater recharge to zones of discharge occurs over distances that can be relatively short. Shallow flow to a depth of tens of metres dominates the overall water balance, and the length of flow paths is relatively short. The analyses of this study indicate that the flow in deeper rock is not regional but rather is a subdued reflection of the local-scale surface topography.