Hospital water supply system may serve as a reservoir of waterborne pathogens, and contaminated water can lead to the occurrence and outbreak of healthcare-associated infection (HAI), which bring great challenge to the prevention and control of HAI. Waterborne pathogens, such as Pseudomonas aeruginosa, Legionella, no-tuberculous Mycobacterium, Acinetobacter, and Stenotrophomonas maltophilia, often propagate and spread through the water supply system. Water temperature, residual chlorine concentration, and biofilm in water supply system are key influencing factors. This article reviews the current situation of waterborne infection, characteristics and influencing factors of water supply system in medical institutions in recent years, as well as related waterborne infection events at home and abroad, so as to bring new insights for the prevention and control of waterborne infection in medical institutions.