Groundwater nitrate (NO3--N) contamination poses a major environmental concern in oasis agriculture in arid regions. Taking the oasis area of the southern Turpan Basin in Xinjiang as the study area, the high and low groundwater level periods were selected as representative hydrological periods. Twenty in situ groundwater samples were collected during each period. We systematically analyzed the spatial, profile, and depth-dependent variations of groundwater nitrate contamination and the associated human health risks. The results show that the mean groundwater NO3--N concentration during the high groundwater level period is 14.46 mg/L, which is significantly higher than that during the low groundwater level period (4.11 mg/L). The exceedance rates above the drinking water standard (>10 mg/L) are 50.0% and 15.0%, respectively. Overall, groundwater nitrate exhibits an anomalous seasonal pattern, with lower concentrations during the low groundwater level period and higher concentrations during the high groundwater level period. Spatially, nitrate contamination shifts from localized point-source distribution during the low groundwater level period to regional-scale dispersion during the high groundwater level period. Shallow groundwater is mainly affected by agricultural activities, whereas localized nitrate contamination in deep groundwater may be associated with cross-aquifer contamination caused by inadequate well sealing. Ionic ratios indicate that chemical fertilizers are the primary source of groundwater nitrate. Regional hydrogeological conditions suggest that nitrate enrichment during the high groundwater level period may result from nitrogen storage in the thick vadose zone and its delayed release through irrigation infiltration. The non-carcinogenic health risk of groundwater nitrate increases significantly during the high groundwater level period, and infants and children are identified as the most susceptible populations. The results provide a scientific basis for the prevention and control of groundwater nitrate contamination in similar arid oasis agricultural regions.