Urban canal swimming events are popular in the Netherlands. In 2015, two city canal swimming events took place, in Utrecht (Utrecht Singel Swim, USS) and in Amsterdam (Amsterdam City Swim, ACS). This prospective study characterizes the health risks associated with swimming in urban waters. Online questionnaires were sent to 160 (USS) and 2,692 (ACS) participants, with relatives of participants who did not swim completing the questionnaire as a control. Swimming water specimens and stool specimens of diarrheic participants in the ACS group were analysed. A total of 49% of USS and 51% of ACS swimmers returned their questionnaires. Nine percent of USS swimmers and 4% of non-swimmers reported gastrointestinal complaints (aRR 2.1; 95% CI: 0.3-16), while a total of 31% of ACS swimmers and 5% of non-swimmers reported gastrointestinal complaints (aRR 6.3; 95% CI: 4.1-9.5). AGI risk among ACS participants was directly related to increasing number of mouthfuls of water swallowed. Various norovirus genotypes were detected in five out of seven stool specimens taken from ACS participants and in all three tested ACS water samples. We conclude that the AGI risk among open-water swimmers in urban areas depends on the circumstances around the event. The epidemiological curve, the statistical association between swimming and AGI, and the microbiological evidence for norovirus in stool and water specimens suggest that AGI outbreak after the ACS event was due to water contamination by multiple norovirus strains, which is possibly linked to sewage overflow due to prior heavy rainfall. There is need for more targeted preventive measurements and recommendations for organizers, municipal authorities and participants to prevent this reoccurring in the future.