Shimabara City in Nagasaki Prefecture, Japan, is located on a volcanic peninsula that has abundant groundwater. Almost all public water supplies use groundwater in this region. For this reason, understanding groundwater characteristics is a pre-requisite for proper water supply management. Thus, we investigated the groundwater chemistry characteristics in Shimabara by use of self-organizing maps (SOMs). The input to SOM was concentrations of eight major groundwater chemical components, namely Cl−, NO3−, SO42–, HCO3−, Na+, K+, Mg2+, and Ca2+ collected at 36 sampling locations. The locations constituted private and public water supply wells, springs, and a river sampled from April 2012 to May 2015. Results showed that depending on the chemistry, surface water and groundwater could be classified into five main clusters displaying unique patterns. Further, the five clusters could be divided into two major water types, namely, nitrate- and non-polluted water. According to Stiff and Piper trilinear diagrams, the nitrate-polluted water represented Ca-(SO4 + NO3) (calcium sulfate nitrate) type, while the non-polluted water was classified as Ca-HCO3 (calcium bicarbonate) type. This indicates that recharging rain water in the upstream areas is polluted by agricultural activities in the mid-slope areas of Shimabara.