The application of synthetic nitrogen (N) fertilizers has boosted crop yields globally. However, it has also imposed on environmental pollution problems. An estimation of actual fertilizer N inputs at the crop field level is needed to establish effective N management plans to control groundwater NO3-N contamination. Here, a survey to collect the types of cultivated crop and fertilizer application rate was conducted during 2016–2018, covering 44,253 small crop fields (7730 ha) in the western part (Hanrim and Hankyung regions) of Jeju Island, South Korea. Foreign vegetables, citrus fruits, and bulb vegetables are the major crop types grown in the total cultivated areas of 2165.6 ha, 1718.7 ha, and 944.9 ha, respectively. For several crops (green garlic, potato, and chives), the over-use of N fertilizers is observed, the amount of which is 1.73–4.95 times greater than the standard fertilizer application rate. The highest level of fertilizer N input is observed for bulb vegetables in both the regions (Hanrim: 500.5 kg/ha, Hankyung: 487.1 kg/ha), with nearly 80% of the N fertilizer input turned into surplus N loading. A comparison between a spatial interpolation map of the fertilizer N input and that of the groundwater NO3-N concentration implies that the excessive use of synthetic fertilizer results in the degradation of groundwater quality by NO3-N. N management plans for the study area are suggested based on the N fertilizer input at the crop field level. This study highlights that sustainable N management plans should be arranged at the crop field level, considering the spatial heterogeneity of N fertilizer use.