Understanding the changes in microbial communities from source to tap water after water stagnation is important for process control and risk management. However, little information is available on the fate of microbial communities from source to tap water after stagnation. This study aims to evaluate the fate of microbial communities from source to tap water for identifying the sources of microorganisms that regrow after water stagnation in premise plumbing. One-year sampling was conducted in raw water (RW), biological activated carbon filtration effluent (BAC), and treated water (TW) from a full-scale drinking water treatment plant. In addition, fresh water (FW) and stagnant water after 24-h stagnation (SW) were collected from eight faucets in the premise plumbing of a building. Sampling was conducted in four seasons in one year. The community structures were analyzed by amplicon sequencing targeting V4 region of 16S rRNA genes. Microbial community between RW, BAC, TW, FW, and SW were significantly distinct. Tracking of operational taxonomic units (OTUs) from source to tap in four sampling events revealed that 87.5–97.5% and 84.6–98.3% of total OTUs contained in RW and BAC were removed, respectively. On the other hand, 5.5–16.3% of total OTUs in TW, which were affiliated with Sphingomonas etc., survived chlorination and increased by more than 10-folds in SW. These bacteria could be chlorine resistant and regrow during distribution. Interestingly, 75.5–85.0% of total OTUs in SW, which were affiliated with Cyanobacteria and Dechloromonas etc., were not detected from all sampling points in treatment plant, suggesting that specific microbial communities were established in premise plumbing. This study thus provides a better understanding of the dynamic changes of microbial communities from source to tap water, which is informative to control microbial regrowth and to achieve biological stability of drinking water.