We summarized the present status of viruses detected in the water system in the human living environment such as sewage, reclaimed water, river water, drinking water, fish and shellfish, and swimming pool water. In addition, the effects of these viruses on human health were discussed based on previous cases of waterborne virus infection and epidemiological data. There are no marked cases of waterborne virus infection in Japan. However, as virus contamination of river water, a source of drinking water, and reclaim from an increase in sewage with advances in urbanization, surveillance of waterborne viruses is needed. We also introduced the present isolation methods of viruses in water. For surveillance of viruses in water, reliable detection methods that can be readily performed in many institutions should be established.