In order to assess the risk of transmission of viral diseases during floods, the viral burden in flooded areas of the city of Dresden (Germany) in August 2002 was investigated. Water samples were collected from 9 sampling sites and tested for the presence of 11 enteric viral pathogens. As a control, water samples from the same sites were analyzed in seasonal intervals over the following year. A total of 36 samples were collected, 92% (33/36) being positive for at least one virus. Adenovirus type 40/41 was the most frequently detected (53%), followed by astrovirus (50%) and enterovirus (50%). In all samples, low levels of bacteriophages were detected with no specificity as to sampling site and season, indicating a moderate river contamination with wastewater. A striking association between water temperature and viral genome detection was observed, as illustrated in August 2002 (mean water temperature of 17.8°, 8 sites positive for 17 viruses), in comparison to November 2002 (mean water temperature of 7.6°, 9 sites positive for 45 viruses). Importantly, hepatitis A viral RNA was not detected in the flooded area. In conclusion, our results indicate no increased risk for transmission of viral diseases through water contact in flooded areas.