Objective To investigate the causes for number of bacterial colonies exceeding the standard in the pure water system found during the acceptance of newly built endoscopy center, and put forward solutions. Methods Water specimens were collected from all steps of pure water preparation and use, the causes for number of bacterial colonies exceeding the standard were identified, disposal measures according to the causes were formulated, and the maintenance time of intensive disinfection effect was monitored. Results The investigation result inferred that the newly laid water pipeline between the outlet of pure water tank and inlet of the endoscope before entering the endoscopic decontamination equipment is the main cause for the bacteria exceeding the standard. According to the causes, combined disposal measures such as pipeline transformation, adding disinfection facilities, cleaning and disinfection of water pipeline and decontamination equipment are formulated. After comprehensive intervention, no bacteria were detected at each sampling point, the endoscopy center was successfully put into use, and the interval of waterline intensive disinfection was determined to be 12 weeks. Conclusion The acceptance before operation of the newly built endoscope center is very important, the new pure water pipeline needs to be flushed before laying to ensure the quality of final rinsing water.