Rooftop rainwater harvesting has received an increased attention as a potential alternative water supply source both in the coastal and arsenic affected rural areas in Bangladesh. Several programs in installing rainwater harvesting systems have been implemented to mitigate the drinking water problem in the coastal and arsenic affected areas in the country. This study was conducted with a view to assess sanitary integrity, microbial contamination and the associated health risk of the currently practiced rooftop rainwater harvesting mainly used for drinking water supply. Sanitary inspection of the rainwater harvesting systems and an extensive sampling of harvested rainwater from the storage reservoirs and laboratory analysis were conducted. The study findings reveal that harvested rainwater was found to microbiologically contaminated to some extend. The disease burden estimated using QHRA model showed a significant microbial health burden associated with drinking untreated rainwater and both viral and bacterial pathogens dominate the microbial disease burden. In context of arsenic mitigation, rainwater harvesting reduces the health risk from arsenic; however it may increase the microbial disease burden much higher than the level of arsenic health risk at 50 μg/L of Bangladesh standard. Microbial risk needs proper attention through the implementation of a water safety plan for safe and sustainable rainwater harvesting in Bangladesh.

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