Alluvial groundwaters in the area where intensive agricultural activity takes place were geochemically investigated to evaluate factors regulating groundwater quality of alluvial aquifers. For this study, 55 groundwater samples were taken from the uniformly distributed irrigation wells and were classified into three distinct groups according to their geochemical characteristics. This study reveals that the groundwater quality and the geochemical characteristics of the clustered groups are consistent with the geology of the area. The samples collected from the area where a thick silt bed overlies the sand aquifer are clustered into Group II and show water quality that is only slightly affected by the contaminants originating from the land surface. However, groundwaters of this group are very high in Fe and Mn levels due to strong anoxic condition caused by the thick silt bed. In contrast, Group I shows water quality largely influenced by agricultural activities (i.e., fertilization, liming) and occurs in the area adjacent to the river where the silt bed is not observed and the sand aquifer is covered with sandy soils. Group III mostly occurs in the upgradient of Group I where a thin, silty soil covers the sand aquifer. In overall, the results show that the clustered groups closely reflect the groundwater susceptibility to the contaminants originated from the land surface. This suggests that groundwater clustering based on water chemistry could be applied to the contamination susceptibility assessment for groundwaters in the agricultural area.