Objective To analyze the causes for the unqualified surveillance result of endoscopic disinfection in a medical institution, summarize the investigation and disposal process, and provide reference for similar events. Methods The causes for the unqualified surveillance result of endoscopic disinfection in the endoscopy center of a medical institution in April 2023 was investigated and analyzed. Measures were adopted, such as stopping using unqualified endoscopes, investigating the cleaning and disinfection operations of endoscopes, maintenance and management of water treatment equipment, and conducting microbiological detection, etc. Disposal measures were formulated based on the existing problems, and problems were rectified. Results The investigation found that the ozone device used for pure water disinfection didn’t work properly; the connection port of the pure water storage tank was broken with water leakage; the waterline was not disinfected after replacing the connection port; and the maintenance of water treatment equipment and waterline disinfection system was incomplete. Twelve disinfected endoscopes were redetected, and 2 were found to be qualified, with a qualified rate of 16.7%. Fifteen pure water specimens were detected. Except that the pure water behind reverse osmosis (RO) membrane was qualified, the remaining 14 specimens, including the final rinse tank for manual cleaning of gastroscopes and colonoscopes, the water inlet of endoscope washer-disinfectors (EWDs), the water outlet of pure water storage tanks, and the return water inlet, were all unqualified, with a qualified rate of 6.7%. The use of pure water equipment was ceased. Endoscope disinfection work was relocated to another endoscope cleaning and disinfection room. All endoscopes were reprocessed, then redetected results were all qualified. Waterline was disinfected with peracetic acid. The raw water treatment equipment was reused since results from three detections were qualified, afterwards, the microbial detection for pure water was strengthened, and the maintenance of the pure water equipment and waterline disinfection were improved. No unqualified pure water occurred. Conclusion Contamination of final rinse water is the main cause for the unqualified surveillance result for endoscopic disinfection quality in this study. Establishing a management system for the operation and maintenance of pure water equipment is crucial to the improvement of endoscopic disinfection quality.