Urban floods can be contaminated with fecal material and pathogens. Evidence on infection risks associated with exposure to waterborne pathogens in urban floods is lacking. We address this gap by assessing the risk of infection from exposure to Giardia lamblia in urban flood water samples in Mexico City using a QMRA. Historical flood data was used to build severity indices and to test for correlations with risk of infection estimates. Results indicate similar maximal pathogen densities in urban flood water samples to those from wastewater treatment plants. Significant positive correlations between risk of G. lamblia infection and severity indices suggest that floods could act as an important source of pathogen transmission in Mexico City. Risk of infection to G. lamblia is greater in the city's periphery, which is characterized by high marginalization levels. We argue that these risks should be managed by engaging citizens, water, and health authorities in decision making.