Heterogeneity in unsaturated soils and sediments is well known to exist at different scales, from microscopic scale to macroscopic scale. Characterization of different types of heterogeneity in deep vadose zones is challenging because of the usual lack of information at such sites. In this paper, we considered a site with detailed geological, chemical, and hydraulic properties measurements throughout an approximately 16-m deep vadose zone consisting of unconsolidated, alluvial deposits typical for the alluvial fans of the eastern San Joaquin Valley, California. At the agricultural site, data were also available for a 7-yr long field fertilization experiment that we used to independently estimate the amount of nitrate stored within the vadose zone at the end of the experiment. Simple mass balance calculations were performed and compared to six conceptually different two-dimensional and three-dimensional vadose zone numerical models that were implemented to represent varying degrees of hierarchical details of heterogeneity. Despite widely differing structure and heterogeneity of unsaturated flow, all models resulted in a narrow range of estimated nitrate storage in the deep vadose zone for near-cyclically repeated water and nitrogen fertilizer applications. Simulated nitrate storage was found to be approximately six to eight times larger than the measured storage at the field. Simulated nitrate variability, while qualitatively similar in pattern, was considerably lower than measured, despite the large simulated hydraulic variability. This study underscores that physical heterogeneity of deep vadose zones may have limited effects on the transfer of conservative contaminants applied repeatedly to the land surface. It also raises questions about our understanding of the chemical fate of nitrate in the vadose zone; and suggests the presence of a significant immobile moisture domain within the deep vadose zone that is not explainable by heterogeneity of Richards equation parameters, yet needs to be considered for simulating nitrate transport under conditions of cyclical infiltration with gravity dominated convective flux.