Vulnerability of groundwater to contamination has typically been addressed by analysis or inference of near-surface hydrologic processes. Yet, in many basins like the Salinas Valley, California, shallow groundwater quality has already been degraded over large areas by nitrates, pesticides, salinity from irrigation, or other contaminants. The ultimate impact of this contamination on deeper groundwater quality during the decades, centuries or millennia to come is a highly relevant issue. We demonstrate an approach to groundwater vulnerability assessment that emphasizes important geologic features in a stochastic-geostatistical framework and incorporates information on both shallow and deep groundwater flow and contaminant transport in the context of a circulating groundwater system. The approach complements more common, shallow investigative approaches, which emphasize source inventory, soil characteristics, and vadose-zone flow and transport. Results from an assessment of groundwater vulnerability to nitrate contamination in the Salinas Valley agree with observed regional patterns in groundwater nitrate concentrations.