Study region: The Coastal California basin aquifer system (CCB), USA. Study focus: Understanding the controls on nonpoint source (NPS) nitrate (NO3−) contamination in groundwater is motivated by the widespread detection of NO3−, implications for human health and aquatic ecosystems, groundwater sustainability, and a growing realization that such understanding across spatial scales promotes management and policy choices that optimize the Water–Energy–Food (WEF) Nexus. In the CCB, the conflicts in the WEF Nexus are apparent because of intensive agricultural practices that have contributed to chronic NO3− loading to groundwater. We evaluate the scale-dependent relations among source, transport, and attenuation (STA) factors that control NPS NO3− contamination in recently recharged CCB groundwater. Logistic regression models are presented for sub-regional and regional model domains. New hydrological insights for the region: Dissolved oxygen (DO) (attenuation) in groundwater is often the most significant STA factor in all model domains, indicating that DO is an important, scale-invariant factor controlling NPS NO3− contamination. Farm fertilizer (source) is also a significant scale-invariant factor, while many of the transport factors are scale-dependent factors. We present vulnerability maps that illustrate the spatial patterns of predicted probability of detected elevated NO3−. Findings here improve knowledge about the scale dependence of STA factors, which help decision makers develop best management strategies and policies that advances groundwater sustainability and optimizes the WEF Nexus.