This work assessed the risks associated with the virological quality of tapwater using a molecular analytical tool manageable in a field survey. It combined a daily epidemiological follow-up of digestive morbidity among a panel of volunteers and a microbiological surveillance of drinking water. RT-PCR was used for detection of enterovirus, rotavirus and astrovirus. 712 cases of acute digestive conditions occurred in the 544 volunteers. 38% (9/24) raw water and 23% (10/44) tap water samples were positive for at least one virus marker with 9/10 positive tap water samples complying with bacterial criteria. No statistically significant association was found between the presence of viral markers and observed incidence of digestive morbidity. However, when an outbreak occurred, enterovirus and rotavirus RNA was detected in the corresponding stored tap water samples. Sequencing of the amplified fragments showed that the rotavirus detected was of bovine origin. This work demonstrated that enteric virus markers were common in tapwater of the study communities (characterised by a vulnerable raw water) despite absence of bacterial indicators. Tangential ultrafiltration coupled to RT-PCR allowed a simultaneous and fast detection of the study viruses from environmental samples. This process is a promising tool usable for virological water surveillance, in as much the corresponding know-how is transferred to the field professionals.