The results of a series of ponded infiltration tests in variably saturated fractured basalt at Box Canyon, Idaho were used to build confidence in conceptual and numerical modeling approaches used to simulate infiltration in fractured rock. Specifically, we constructed a dual-permeability model using TOUGH2 to represent both the matrix and fracture continua of the upper basalt flow at the Box Canyon Site. A consistent set of hydrogeological parameters was obtained by calibrating the model to infiltration front arrival times in the fracture continuum as inferred from Br− samples collected from fracture–borehole intersections observed during the infiltrating tests. These parameters included the permeability of the fracture and matrix continua, the interfacial area between the fracture and matrix continua, and the porosity of the fracture continuum. To calibrate the model, we multiplied the fracture–matrix interfacial area by a factor between 0.1 and 0.01 to reduce imbibition of water from the fracture continuum into the matrix continuum during the infiltration tests. Furthermore, the porosity of the fracture continuum, as calculated using the fracture aperture inferred from pneumatic-test permeabilities, was increased by a factor of 50 yielding porosity values for the upper basalt flow in the range of 0.01 to 0.02. The fracture-continuum porosity was a highly sensitive parameter controlling the arrival times of the simulated infiltration fronts. Porosity values are consistent with those determined during the Large-Scale Aquifer Pumping and Infiltration Test at the Idaho National Engineering and Environmental Laboratory.