Abstract Background Climate change is expected to increase the chance of extreme rainfall events in the Northern Hemisphere and herewith, there is an increased chance of urban pluvial flooding. Urban pluvial flooding often consists of street flooding and/or flooding of combined sewerage systems, leading to contamination of the floodwater with several gastrointestinal and/or respiratory pathogens. An increase in flooding events therefore pose a health risk to those exposed to urban floodwater. We studied the association between exposure to pluvial floodwater and acute gastroenteritis (AGE) and acute respiratory infection (ARI). Methods We performed a retrospective, cross-sectional survey during the summer of 2015 in 60 locations in the Netherlands with reported flooding. Two weeks after the flooding, questionnaires were sent to households in these locations, collecting data on self-reported AGE and ARI and information on floodwater exposure in the previous 2 weeks. Multivariable generalized estimating equations (GEE) regression models, accounting for the clustered data structure, were used to identify risk factors for AGE and ARI. Results In total, 699 households with 1,656 participants (response rate 21%) returned the questionnaire. Contact with floodwater was significantly associated with AGE (aOR 4.2, 95%CI 2.1–8.4) and ARI (aOR 3.3, 95%CI 2.0–5.4). Risk factors for AGE were skin contact with floodwater (aOR 4.0, 95%CI 1.8-9.0), performing post-flooding cleaning operations (aOR 8.6, 95%CI 3.5-20.9) and cycling through floodwater (aOR 2.3, 95%CI 1.0-5.0). Skin contact with floodwater (aOR 3.6, 95%CI 1.9-6.9) and performing post-flooding cleaning operations (aOR 5.5, 95%CI 3.0-10.3) were identified as risk factors for ARI. Conclusions Results suggest an association between direct exposure to pluvial floodwater and AGE and ARI. As it is predicted that the frequency of pluvial flooding events will increase in the future, there is a need for flood-proof solutions in urban development and increased awareness among ...