This second edition of the Guide to Investigating Waterborne Disease Outbreaks compiles practical information useful for investigations. It draws on feedback and the expertise of epidemiologists, public health engineers, and microbiologists. It is divided into three sections corresponding to the three phases of the investigation: preparation, alert and mobilization, in-depth studies, and lessons learned. A coordinated implementation of epidemiological, environmental, and microbiological investigations (in patients and in the water) is crucial both for confirming the waterborne origin and taking rapid precautionary measures, as well as for the successful completion of the investigations (identification of causes, corrective measures, and pathogens). This guide is intended for staff at regional health agencies and Public Health France regional response teams who may be responsible for or involved in investigating these outbreaks. It may also be useful to other stakeholders, including those responsible for water production or distribution. It complements the resource document Detection and Investigation of Outbreaks of Waterborne Infections: An Integrated Environmental and Public Health Approach, which remains relevant.