Factor analysis is applied to 28 groundwater samples collected from wells in the coastal blackfoot disease area of Yun-Lin, Taiwan. Correlations among 13 hydrochemical parameters are statistically examined. A two-factor model is suggested and explains over 77.8% of the total groundwater quality variation. Factor 1 (seawater salinization) includes concentrations of EC, TDS, Cl(-), SO(4)(2-), Na(+), K(+) and Mg(2+), and Factor 2 (arsenic pollutant) includes concentrations of Alk, TOC and arsenic. Maps are drawn to show the geographical distribution of the factors. These maps delineate high salinity and arsenic concentrations. The geographical distribution of the factor scores at individual wells does not reveal the sources of the constituents, which are instead, deduced from geological and hydrological evidence. The areas of high seawater salinization and arsenic pollution correspond well to the groundwater over-pumping area. Over-pumping of the local groundwater causes land subsidence and gradual salinization by seawater. The over-pumping also introduces excess dissolved oxygen that oxidizes the immobile minerals, releases arsenic by reductive dissolution of arsenic-rich iron oxyhydroxides and increases the arsenic concentration in water. The over-extraction of groundwater is the major cause of groundwater salinization and arsenic pollution in the coastal area of Yun-Lin, Taiwan.