Recurrent flooding is a serious but unquantified public health threat in megacities throughout the developing world. This paper provides the first causal estimates of the mortality impacts of daily rainfall shocks and urban flooding, using novel data from one of the world’s largest cities— Mumbai, India. We obtain the universe of person-level mortality records for Mumbai between 2006 and 2015 and match these to highly localized measures of sub-daily rainfall. High rainfall days cause large increases in mortality that persist over the subsequent five weeks. The impacts are greater in low elevation areas and during high tides, suggesting that the effects of flooding are driving these results. Rainfall explains a substantial portion of Mumbai’s overall mortality rate, comparable to the death rate from all cancers. Children under five and slum residents are the most highly affected. Our study highlights an important and previously undocumented cost of routine rainfall and urban flooding, which has implications for current policy and for damage projections under future climate change.