The purpose of this study is to delineate the main contributions controlling the chemical composition of groundwater and spring water samples at Jeju Island, South Korea. Groundwater and spring water can be grouped as three chemical types: Fresh water (Ca, Na-HCO3), sea water mixing (Na-Cl, SO4) and contamination (Ca-NO3, Cl). By factor analysis, three factors can explain about 87% of chemical variances: Factor 1 (Na+ and Cl−), factor 2 (NO3−), and factors 3 (HCO3−), which are regarded as indicative ions of sea water mixing, contamination and mineral-water interaction, respectively. Sea water intrusion in the southeastern area of Jeju Island is due to downward distribution of Seogwipo Formation, which plays a role as an aquiclude preventing sea water intrusion in other areas, under sea level at the southeastern coastal area. Nitrate contamination is likely to be affected by pollution sources, i.e., agricultural activities, horse farms and municipal sewage. Thermodynamic saturation index indicates that most of waters are undersaturated with respect to major minerals, which may result from insufficient reaction time within a permeable aquifer. The unsaturation state corresponds to low load scores of Ca, Mg, Na, K, and SiO2 in factor 3, which means a low contribution of mineral-water interaction.