The objective of this work was to investigate flow and transport in a layered, variably saturated system consisting of both fractured rock and sedimentary material during focused infiltration from the surface. Two tracer tests were performed using the Vadose Zone Research Park (VZRP) at the Idaho National Laboratory (INL). The first test occurred under quasi-steady-state conditions and the second was initiated in a much drier system and thus provided information regarding flow and transport under transient conditions. A one-dimensional analytical model was used to fit breakthrough curves resulting from the two tracer tests. The results of this modeling provide insight into the nature of flow in the fractured basalt, surficial alluvium, and sedimentary interbeds that comprise the vadose zone of the eastern Snake River Plain. Flow through the fractured basalt is focused and preferential in nature, and multiple flow paths arise due to numerous fractures functioning as transmissive pathways in addition to flow splitting along geologic contacts. Flow velocities were significantly higher during the test with the wetter flow domain, presumably due to increases in hydraulic conductivity associated with higher water contents of the geologic materials. Perching was observed above the alluvium–basalt contact and above the lower boundary of a locally continuous sedimentary interbed. The perching behavior between the two contacts was fundamentally different; the perched layer above the alluvium–basalt contact was neither laterally extensive nor temporally persistent in the absence of infiltration from the surface. In contrast, the perched layer along the interbed was significantly thicker and gave rise to lateral flow over distances on the order of hundreds of meters. Vertical transport is shown to occur predominantly through the main bulk of the sedimentary material of the interbed; lateral flow appears to occur primarily in the fractured basalt directly above the interbed.