Household water purifiers are increasingly used to treat drinking water at the household level, but their influence on the microbiological safety of drinking water has rarely been assessed. In this study, representative purifiers, based on different filtering processes, were analyzed for their impact on effluent water quality. The results showed that purifiers reduced chemical qualities such as turbidity and free chlorine. However, a high level of bacteria (102–106 CFU/g) was detected at each stage of filtration using a traditional culture-dependent method, whereas quantitative PCR with propidium monoazide (PMA) treatment showed 106–108 copies/L of total viable bacteria in effluent water, indicating elevated microbial contaminants after purifiers. In addition, high-throughput sequencing revealed a diverse microbial community in effluents and membranes. Proteobacteria (22.06–97.42%) was the dominant phylum found in all samples, except for purifier B, in which Melainabacteria was most abundant (65.79%). For waterborne pathogens, Escherichia coli (100–106 copies/g) and Pseudomonas aeruginosa (100–105 copies/g) were frequently detected by qPCR. Sequencing also demonstrated the presence of E. coli (0–6.26%), Mycobacterium mucogenicum (0.01–3.46%), and P. aeruginosa (0–0.16%) in purifiers. These finding suggest that water from commonly used household purifiers still impose microbial risks to human health.