Little empirical evidence exists about the spatial distribution of NO3–N in deep vadose zones and about the associated fate and transport of NO3–N between the root zone and the water table. We investigated NO3–N occurrence in a deep alluvial vadose zone and its relation to geologic site characteristics, hydraulic properties, and fertilizer application rates via an intensive three-dimensional core-sampling campaign beneath an irrigated orchard in semiarid Fresno County, California. Statistical and geostatistical analyses were used to determine spatial variability of NO3–N and water content, to estimate total NO3–N mass in the vadose zone beneath each of three fertilizer treatments, and to compare NO3–N occurrence with that predicted from standard agronomic analysis of N and water flux mass balances. Vadose zone NO3 was highly variable and lognormally distributed. Fertilizer treatment had a significant effect on NO3–N levels in the vadose zone. In all cases, deep vadose zone N mass estimated by kriging measured data totaled only one-sixth to one-third of the mass predicted by the N and water flux mass balance approach. Vadose zone denitrification estimates could not account for this discrepancy. Instead, the discrepancy was attributed to highly heterogeneous flux conditions that were not accounted for by the mass-balance approach. The results suggest that spatially variable vadose zone flow conditions must be accounted for to better estimate the potential for groundwater NO3 loading.