Small-scale distributed water purifiers (SSDWPs), providing better quality drinking water, are popularly used both in homes and in the public domain. Non-continuous operation leads to water stagnation and ultimately induces microbial contamination. However, information related to such contamination in these purifiers is reported scarcely. In the present study, an SSDWP, consisting of sand filtration (SF), granular activated carbon (GAC), and ultrafiltration (UF) processes, was established to explore microbial changes induced by water stagnation, based on the aspects of bacterial count, microbial size, microbiome and pathogenic communities. Our results primary showed that: first, compared with drinking water distribution system (DWDS), bacterial counts increased more rapidly in SSDWPs, growing to > 500 cfu/mL after 2.5 h stagnation. The proportion of intact cells also increased with stagnation time. Conversely, microbial size decreased with stagnation time according to changes in forward scatter detected using flow cytometry. Second, microbiome evolution followed the isolated island model, while in stagnated DWDS, microbiome evolved according to the continent island model, and the former had higher abundance of biodiversity. Furthermore, stagnation evidently caused microbiome changes in each unit, and spatial differences contributed to microbiome dissimilarity more significantly than temporal differences. Third, Mycobacterium was the dominant pathogenic genus in the SF and GAC units while Acinetobacter was the most abundant in the UF unit. Pathogenic risks increased with water stagnation time and lower nutrients level contributed to pathogenic community richness. Therefore, terminal disinfection of SSDWPs is strongly advised.