A sophisticated dual-permeability flow model of the T-tunnel complex, Rainier Mesa, Nevada National Security Site, was developed and calibrated to facilitate predictions of radionuclide transport from underground nuclear tests within a perched zone of saturation downward through a series of variably saturated, sparsely fractured and faulted Tertiary tuff units to a regional flow system. The hydrogeologic complexity of the site necessitated a multistage calibration effort to capture the dominant flow characteristics of the site including: laterally and vertically extensive saturation in the Tertiary volcanics, pressure heads consistent with water level measurements, variably saturated flow conditions involving a thin unsaturated zone situated between two saturated zones, unsaturated Paleozoic carbonates located immediately adjacent to saturated Tertiary volcanic units, and fracture saturations congruent with field observations that range from fully saturated to dry. The incorporation of discontinuous fault networks into the dual-permeability model played a key role in reproducing the salient hydrologic features of the site. Successful model reproduction of observed cumulative tunnel discharge volume and tunnel discharge rates before tunnel sealing served as a novel transient test of the ability of the discontinuous fault networks to realistically honor field-scale fault network connectivity and permeability. The excellent reproduction of field observations by the numerical model, and the uniqueness of the primary parameters used to calibrate the model, demonstrate the advantage of incorporating discontinuous fault networks over equivalent fracture properties in sparsely fractured, dual-permeability media.