The Choushui River Alluvial Fan is situated on the western Taiwan. Groundwater is one of the most important sources of water resources in the Choushui River Alluvial Fan and is widely used for irrigation and aquaculture because of its abundant supply. However, a long-term survey of groundwater quality in the Choushui River Alluvial Fan area has revealed obvious contamination of the groundwater in some areas, with measured concentrations of some quality parameters in excess of the acceptable levels regulated by the Taiwan Environmental Protection Administration. Establishing a sound plan for groundwater quality protection in the Choushui River Alluvial Fan area is imperatively important. Therefore, efforts for monitoring groundwater quality are required as part of the critical steps to protect groundwater quality but are expensive and time consuming. The connection between shallow aquifer and the landscape above it supports the premise that groundwater quality may be affected by the overlying land uses, thus investigation on the relationship between land use and the groundwater quality is gaining increasing attention. The objective of this study targets to characterize the relationship of land use on groundwater quality in the Choushui River Alluvial Fan area by applying the factor analysis to analyze 14 groundwater quality parameters, 9 area percentage for different land use categories in the neighborhood of the wells and the length of 4 types different geological material in the unsaturated zone. The results suggest that a six-factor model can explain 70.35% of the total variance and three factors among six factors model involve the different land uses while other parameters are attributed by natural processes. The arsenic concentration shows significant linkage to water conservation of land use and fine sediment of the unsaturated zone. E. coli pollution is associated with livestock and aquaculture. Nitrate pollution is found in the area of dryland crops. Maps of factor score are also demarcated to describe the areas that more vulnerable to contamination from land use, prioritize the areas where more intensive monitoring might be needed, evaluate current land use practice or adopt new measures to better prevent or control the potential pollution sources.