Not only application of fertilizer but seawater intrusion seems to affect the groundwater quality in a coastal farming area. In this study, field surveys were conducted to examine the characteristics of groundwater quality over a wide coastal area with farming greenhouses. Principal component analysis revealed that the information contained in the original data set was explained up to 75.8% by only four principal components, and that groundwater quality in the area was affected mainly by soil characteristics, application of fertilizer and seawater intrusion. The observation field was divided into three categories corresponding to the geographical information through the cluster analysis: (1)In the eastern, central and western part of Higashimorogi district, neither application of fertilizer nor seawater intrusion affected groundwater quality except three wells where the influence of fertilizer was large. (2)Characteristics of the soils were supposed to be different in northeastern part of Higashimorogi from other districts. (3)In Kodono district, not only seawater intrusion but application of fertilizer affected the water quality. It was also demonstrated that the effect of seawater intrusion on groundwater quality appeared more remarkably in a well nearer the coast and in a deeper well having the almost same distance from the coast.