Nitrate pollution in groundwater is a serious problem in Shimabara Peninsula, Nagasaki, Japan. A better understanding of the hydrogeochemical evolution of groundwater in vulnerable aquifers is important for health and environment. In this study, groundwater samples were collected at 12 residential and 57 municipal water supply wells and springs in July and August 2018. Nitrate (NO3-N) concentration at eight sampling sites (12%) exceeded Japanese drinking water standard for NO3 + NO2-N (10 mg L-1). The highest nitrate concentration was 19.9 mg L-1. Polluted groundwater is distributed in northeastern, northwestern, and southwestern areas, where land is used for intensive agriculture. Correlation analysis suggests that nitrate sources are agricultural fertilizers and livestock waste. Dominant groundwater chemistry is (Ca+Mg)-HCO3 or (Ca+Mg)-(SO4+NO3) type. Groundwater with higher nitrate concentration is of (Ca+Mg)-(SO4+NO3) type, indicating nitrate pollution affecting water chemistry. Principal component analysis extracted two important factors controlling water chemistry. The first principal component explained dissolved ions through water-rock interaction and agricultural activities. The second principal component explained cation exchange and dominant agricultural effects from fertilizers. Hierarchical cluster analysis classified groundwater into four groups. One of these is related to the dissolution of major ions. The other three represent nitrate pollution.