A numerical model of a fractured basalt vadose zone has been developed on the basis of the conceptual model described by Faybishenko et al. [this issue]. The model has been used to simulate a ponded infiltration test in order to investigate infiltration through partially saturated fractured basalt. A key question addressed is how the fracture pattern geometry and fracture connectivity within a single basalt flow of the Snake River Plain basalt affect water infiltration. The two-dimensional numerical model extends from the ground surface to a perched water body 20 m below and uses an unconventional quasi-deterministic approach with explicit but highly simplified representation of major fractures and other important hydrogeologic features. The model adequately reproduces the majority of the field observation and provides insights into the infiltration process that cannot be obtained by data collection alone, demonstrating its value as a component of field studies.