This research examined the microbiological quality of drinking water distribution systems typically encountered in First Nation in Canada. Fecal bacteria and a wide range of antibiotic resistance genes (ARGs) were frequently present in tap water of a community that relies on lake water as the source water to its water treatment plant, whereas this was not the case in communities that rely on groundwater. Fecal bacteria and ARGs were predominantly detected in tap water of homes that had water distributed by a truck for storage in underground cisterns, and not in treated water of homes with piped water. Cistern samples that tested positive for fecal bacteria had free residual chlorine concentrations less than 0.2 mg/L, which is required to suppress microbial growth. We are urging all governments in Canada to strategize how to alternatively deliver clean, running drinking water to families living in these homes.