We present a comprehensive field and modeling effort to characterize the transient transport of nitrate in deep alluvial vadose zones including physical, geological, and geostatistical characterization of the spatial variability of the unsaturated sediments. The extensively characterized “Kearney” field site, a former irrigated nectarine orchard in semi-arid Fresno County, California, is used to explicitly consider heterogeneity at two scales: the Darcy scale (heterogeneity within lithofacies), and the lithofacies scale (heterogeneity between lithofacies). We compare two transient flow and transport models, representing a seven-year history of hydrologic and agronomic events at the field site. In one model, within-lithofacies heterogeneity is neglected, whereas between-lithofacies heterogeneity is explicitly represented. In the second model, we consider heterogeneity at both scales, the Darcy scale and the lithofacies scale. We compare the effect of these two representations on water flow and NO3-N transport in a deep alluvial vadose zone beneath an irrigated orchard. Estimated NO3-N levels in the vadose zone and NO3-N leaching to groundwater are significantly different between the fertilizer treatments, yet are nearly identical between the two models. Neither model is capable of reproducing the low nitrate mass found within the vadose zone at the field site suggesting that key processes are not adequately represented. We hypothesize that the two-dimensional representation, the use of scaling factors to represent soil physical heterogeneity, and numerical dispersion may have significant limitations in nitrate transport modeling through heterogeneous vadose zones.