Incidence of various diseases can increase following a flood. We aimed to identify professionals in Copenhagen who became ill after contact with 2 July 2011 floodwater/sediment and determine risks and protective factors associated with illness. We conducted a cohort study of employees engaged in post-flood management activities. Participants completed a questionnaire collecting information about demographics, floodwater/sediment exposure, compliance with standard precautions, and symptoms of illness. Overall, 257 professionals participated, with 56 (22%) cases. Risk of illness was associated with not washing hands after floodwater/sediment contact [relative risk (RR) 2∙45], exposure to floodwater at work and home (RR 2∙35), smoking (RR 1∙92), direct contact with floodwater (RR 1∙86), and eating/drinking when in contact with floodwater (RR 1∙77). Professionals need to follow standard precautions when in contact with floodwater/sediment, especially proper hand hygiene after personal protective equipment use and before eating/drinking and smoking.