Climate change may increase the incidence of waterborne diseases due to extreme rainfall events, and consequent microbiological contamination of the water source and supply. As a result of the complexity of the pathways from the surface to the consumer, it is difficult to detect an association between rainfall and human disease. The water supply of a Hungarian city, Miskolc (174,000 inhabitant), is mainly based on karstic water, a vulnerable underground water body. A large amount of precipitation fell on the catchment area of the karstic water source, causing an unusually strong karstic water flow and flooding, and subsequent microbiological contamination. The presence of several potential sources of contamination in the protective zone of the karstic water source should be emphasized. The water supplier was unprepared to treat the risk of waterborne outbreak caused by an extreme weather event. Public health intervention and hygienic measures were taken in line with epidemiological actions, focusing on the protection of consumers by providing safe drinking water. The contamination was identified, and measures were taken for risk reduction and prevention. This case study underlines the increasing importance of preparedness for extreme water events in order to protect the karstic water sources and to avoid waterborne outbreaks.