Objective To conduct microbiological monitoring before the operation of the purified water treatment system in a newly-built endoscopy center, comprehensively analyze the causes for the standard-exceeding results of microbial detection of final rinse water, propose solutions, and provide reference for handling similar events in the future. Methods Microbial detection data of the final rinse water in the newly-built digestive endoscopy center of a tertiary first-class general hospital in Beijing from April to July 2024 were monitored. The potential causes for standard-exceeding results of microbial detection of final rinse water were analyzed from the perspectives of equipment maintenance and management of the purified water treatment system as well as the improvement of cleaning and disinfection methods for the purified water supply pipeline in the endoscopy center, targeted improvement mea-sures were proposed accordingly. Results The microbial monitoring result of final rinse water in the newly-built digestive endoscopy center built in April 2024 was 1 400 CFU/100 mL, with the main bacterial type being Cupriavidus pauculus. After five rounds of improvement measures and rechecks, microbial monitoring result of the final rinse water in the newly-built endoscopy center was 0 CFU/100 mL, with a qualification rate of 100%. Analysis suggested that the main causes for the standard-exceeding results of microbial detection of final rinse water were due to the damage of the reverse osmosis membrane, lack of cleaning for the pure water storage tank before use, and non-standard cleaning and disinfection process for the pure water supply pipeline, after targeted improvement, the problem was solved. Conclusion Medical institutions should continuously conduct periodic monitoring on water used for endoscope, regularly perform cleaning and disinfection of the purified water treatment system, standardize cleaning and disinfection procedures, ensure medical quality and patient safety.