We quantitatively investigated the relationship between flood conditions and the incidence of diarrhoea caused by flooding in Dhaka City, Bangladesh, by using a two-dimensional flood simulation model. We performed flooding simulation in target areas, and the simulated results were compared to diarrhoeal morbidity. Diarrhoea causes were assessed through home-visit morbidity surveys; these surveys were conducted three times in different phases of the rainy season (pre, mid and post-monsoon) in 10 low-income communities in flood-prone areas of Dhaka City, targeting children below five years of age. The results revealed that flooding influences the morbidity of diarrhoea, as increased morbidity was identified in almost all communities in the mid-monsoon season. However, cases with a predisposition of diarrhoea such as socioeconomic status were also identified, as morbidity was observed in pre- and post-monsoon seasons when flooding did not occur. Furthermore, morbidity was higher in areas with maximum flooding depth of 0.7–1.2 m than that in areas with maximum flooding depth of 0.1–0.2 m in each season. Consequently, we found that the gradient of diarrhoeal vulnerability is affected by predisposing factors such as socioeconomic status, and its influence is maintained throughout the rainy season.