An increase in waterborne illnesses related to floodings has been reported all over the world, especially in developing countries. In Dhaka City, floodings occur almost every year due to severe rainfall without adequate drainage. Waterborne illnesses spread easily in an unhygienic environment. This study developed a method to estimate the incidences of diarrhoea associated with floodings using a flooding analysis. We performed a flooding analysis using a numerical flooding simulation model and investigated the relationship between floodwater depth and diarrhoea incidence. The incidence of diarrhoea was assessed through a mortality and morbidity survey conducted in 10 low-income communities in flood-prone areas of Dhaka City. The results showed a positive correlation between floodwater depth and diarrhoea incidence. This indicates that a flooding analysis method can be used to estimate diarrhoea incidence.