Because of the limited surface water on the Pingtung Plain, Taiwan, the plain's residents frequently extract groundwater to meet their daily household water demands. The residents may experience gastrointestinal infections due to incidental ingestion of groundwater with fecal pollution. This study used indicator kriging (IK) and quantitative microbial risk analysis (QMRA) to assess the health risks of using groundwater for household cleaning and horticultural irrigation on the Pingtung Plain. First, IK was employed to determine the conditional cumulative distribution function (CCDF) of groundwater Escherichia coli (E. coli). Nonparametric Monte Carlo simulation based on established CCDF was then adopted to characterize the distributions and uncertainty of groundwater E. coli. Finally, QMRA was employed to determine health risks of groundwater use for household cleaning and horticultural irrigation, and the 95th percentiles of the risk distributions were calculated to obtain a representative risk. The study results indicated that the health risks of groundwater use ranged from 3.95 × 10 to 2.49 × 10 infections/user/year and exceeded the acceptable level, 1 × 10 infections/user/year, in most of the aquifers. Accordingly, residents of this plain should not directly extract groundwater for use in daily life.