To use shallow groundwater NO3–N concentration as an indicator of groundwater quality requires understanding its patterns, correlations, and controls across space and time. Within a study comparing variable-rate and uniform N management, our objectives were to determine groundwater NO3–N patterns and correlations at various spatial and temporal scales and their association with natural controls and N management. Experiments in a random, complete block design were conducted in a 2-yr crop rotation in North Carolina that included one variable-rate and two uniform N management treatments to wheat (Triticum aestivum L.) and corn (Zea mays L.). We measured groundwater NO3–N and depth every 2 wk at 60 well nests, sampling the 0.9- to 3.7-m depth. Field-mean NO3–N varied with time from 5.5 to 15.3 mg NO3–N L−1. These variations were correlated primarily with concurrent changes in water table elevation and depth. Mean NO3–N exhibited two preferred states: high when the water table was shallow and low when the water table was deep. Temporal NO3–N fluctuations greatly exceeded treatment effects. Treatments appeared to affect NO3–N temporal covariance structure. Groundwater NO3–N spatial patterns and correlations were associated mostly with saturated hydraulic conductivity and water table fluctuations and appeared influenced by subsurface lateral flow. When treatment effects became consistently significant later in the study, they overrode natural controls, and NO3–N was spatially uncorrelated or exhibited shorter spatial correlation ranges and patterns associated predominantly with treatments.