Groundwater serves as a major drinking water source due to inadequate piped supplies in Indonesia. To eliminate the health risks associated with groundwater consumption, boiling appears as the most suitable and cost-effective treatment technique and widely practiced in Indonesia. Despite treatment efforts, inappropriate water storage and handling practices pose a higher risk of recontamination after treatment. The objective of this study was to analyse the effectiveness of groundwater boiling and treated water recontamination in Metro and Bekasi cities, Indonesia. Groundwater at the source and point of use samples were surveyed and assessed from a total of 116 households, resulting in 60% and 35% E. coli contamination, respectively. Paired testing involving boiling observed a reduction in microbial risk for 45% of households. However, 12% samples had an increase in risk even though boiling was reported. Furthermore, E. coli concentration at source prior to boiling and point of use after boiling showed a statistically significant difference (N=111, P<0.01). This study demonstrated the effectiveness of boiling in reducing contamination, although recontamination was evident in some cases, likely due to unsafe water storage and unhygienic environment.