The aim of this study was to determine whether testing for faecal contamination of water through evaluation of traditional bacteriological indicators, as per Directive EEC 76/160, effectively correlates with the presence of viruses in water. The study was performed both on water samples and bivalve molluscan shellfish (Mytilus galloprovincialis) with the further objective of evaluating whether mussels could be used as bioindicator organisms for assessing faecal pollution of water. Overall, 23 sea-water samples and the same number of mussels, taken from three sites along the Salento coast in southern Italy, were analysed to detect total and faecal coliforms, faecal streptococci, E. Coli, Salmonella and enteric viruses. The results of the study confirm that viruses and bacteria do not always follow the same trend. In fact, in one of the two water samples which tested positive for viruses, bacteriological indicators of faecal contamination were found to be below the limits established by current legislation and Salmonellae were absent. Similar results were obtained in the sample of mussels which tested positive for viruses. Conflicting results were obtained in the two examined matrices. This study highlights the importance of searching for viruses in the water environment and the possibility of using mussels as bioindicators for monitoring virological quality of coastal sea-waters.