A system for the retrospective detection of clusters of acute gastroenteritis requiring medical care (AGEC) linked to a plausible waterborne source has been in place across all regions of France since 2019. This national system relies on data from the French national health insurance system to identify cases of GEAm since 2010 and on the Sise-Eaux database (Health and Environment Information System on Drinking Water) to characterize exposure to tap water. The system’s main objectives are to identify water systems at risk of microbiological contamination and to improve understanding of the impact of waterborne disease outbreaks and associated risk factors. Between 2010 and 2022, 145 waterborne GEA outbreaks were recorded in France, 124 of which were newly detected by this system compared to the reporting system. The affected drinking water systems serve 790,000 people, and the circumstances of the contamination have helped identify vulnerabilities in water resources, treatment, and distribution. Greater participation in the system would improve protection for tap water consumers regarding microbiological risk.