Mangroves are vital part of the local economy for some communities in the region of Vitória, Brazil. Oysters, mussels, and crabs, which are naturally abundant in the mangroves, are harvested and largely consumed in restaurants and by the population. In recent years, unusually high rates of annual gastroenteritis cases have been reported in the region suggesting an association between the consumption of contaminated shellfish and the development of gastrointestinal diseases. The objective of this study was to evaluate water samples and mussels collected in the mangrove region using bacterial indicator Escherichia coli and enteric viruses (adenovirus, rotavirus, and norovirus). Our results showed that the region of study is impacted by a continuous discharge of domestic sewage. Although E. coli was detected at low densities in water samples, mussels were shown to be 400 times more contaminated throughout the period of the study. Adenovirus and rotavirus genomes were detected by nested-polymerase chain reaction respectively in 76 and 88% of water samples and 100% of mussel samples. Norovirus was found in 4.8% of water samples and was not detected in the mussels. The screening of bivalves for the presence of health-significant enteric viruses can help in the prevention of outbreaks among shellfish consumers and contribute to improvement of the estuarine environment.