Owing to limited surface water during a long-term drought, this work attempted to locate clean and safe groundwater in the Choushui River alluvial fan of Taiwan based on drinking-water quality standards. Because aquifers contained several pollutants, multivariate indicator kriging (MVIK) was adopted to integrate the multiple pollutants in groundwater based on drinking- and raw-water quality standards and to explore spatial uncertainty. According to probabilities estimated by MVIK, safe zones were determined under four treatment conditions—no treatment; ammonium–N and iron removal; manganese and arsenic removal; and ammonium–N, iron, manganese, and arsenic removal. The analyzed results reveal that groundwater in the study area is not appropriate for drinking use without any treatments because of high ammonium–N, iron, manganese, and/or arsenic concentrations. After ammonium–N, iron, manganese, and arsenic removed, about 81.9–94.9% of total areas can extract safe groundwater for drinking. The proximal-fan, central mid-fan, southern mid-fan, and northern regions are the excellent locations to pump safe groundwater for drinking after treatment. Deep aquifers of exceeding 200 m depth have wider regions to obtain excellent groundwater than shallow aquifers do.