As part of the Canadian Nuclear Fuel Waste Management Program, the Underground Research Laboratory (URL) was constructed approximately 400-m below ground surface in the granitic rock of the Lac du Bonnet batholith situated in southeastern Manitoba, Canada. Site characterisation activities prior to, during and following URL excavation has lead to the creation of an extensive geologic, structural, geochemical and hydrogeological database for the research facility. In part, this database has been used to develop a conceptual geoscientific model for the Moderately Fracture Rock (MFR) Experiment, which is conducted on the 240-m level of the URL. The MFR Experiment is exploring the validity of the Equivalent Continuum Model (ECM) approach in settings where flow and mass transport occurs principally within a hierarchical network of interconnected fractures. In this paper, the validity of an alternative conceptual approach based on a Dual Continuum Model (DCM) is examined. The three-dimensional URL-scale flow and transport DCM model employs dual-porosity dual-permeability theory under variably-saturated conditions, and also integrates two-dimensional overland flow induced by rainfall events. By assigning fracture and matrix properties consistent with available data, and by making use of the three-dimensional geological and structural interpretations of the URL, it is shown that the rapid hydraulic responses observed at depth due to individual precipitation events can only be explained by inclusion of the fracture continuum. While much of the domain is sparsely fractured or consists of intact rock, the infiltration that occurs on the land surface at locations where the identified fracture zones outcrop yields a rapid hydraulic response at depth due to the moderate hydraulic conductivity, but low storage of these zones. It is also shown that inclusion of the drawdown effects of URL main shaft excavation is necessary in order to obtain agreement with observed hydraulic head data.