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Healthy longevity is associated with many factors, however, the potential correlation between longevity and microbiota remains elusive. To address this, we explored environmental microbiota from one of the world’s longevity townships in China. We used 16S rRNA gene high-throughput sequencing to analyze the composition and function of water microbiota. The composition and diversity of water microbiota significantly differed between the towns. <i>Lactobacillus</i>, <i>Streptococcus</i>, <i>Bacteroides</i>, <i>Faecalibacterium</i>, and <i>Stenotrophomonas</i> were only dominant in Xinpu, a town with an exceptionally high centenarian population. Several biomarkers were identified, including <i>Flavobacterium</i>, <i>Acinetobacter</i>, <i>Paracoccus</i>, <i>Lactobacillales</i>, <i>Psychrobacter</i>, <i>Bacteroides</i>, <i>Ruminococcaceae</i>, and <i>Faecalibacterium</i>, and these shown to be responsible for the significant differences between towns. The main species contributing to the differences between towns were <i>Cyanobacteria</i>, <i>Cupriavidus</i> and <i>Ralstonia</i>. Based on KEGG pathways showed that the predicted metabolic characteristics of the water microbiota in Xinpu towns were significantly different to those of the other towns. The results revealed significant differences in the composition and diversity of water microbiota in the longevity township. These findings provide a foundation for further research on the role of water microbiota in healthy longevity.