Using regional geographic, geologic, surface and subsurface hydrologie, and geophysical data for the Tono area in Gifu, Japan, we develop a numerical model to simulate subsurface flow and transport in a 4 km x 6 km x 3 km thick fractured granite rock mass overlain by sedimentary layers. Individual fractures are not modeled explicitly. Rather, large-scale features such as lithologic layering and major fault zones are assigned deterministically, and continuum permeability and porosity distributions are assigned stochastically, based on well-test data and fracture density measurements. The model simulates the steady-state groundwater flow through the site, and then stream trace analysis is used to calculate travel times to the model boundary from specified points. The study is being conducted as a part of the site characterization effort for the Mizunami Underground Research Laboratory in Japan. Predicted travel times range from 1 to 25 years. Several other research groups also developed models based on the same data set, and comparison between different models' results highlight which aspects of site characterization need to be improved in order to increase confidence in model predictions. A wide range in travel times obtained by the different research groups (1-10,000,000 years) can be largely attributed to orders of magnitude differences in the effective porosity used for the fracture network. This underscores the importance of improved porosity estimates as a key component of future site characterization.