Several protocols have been described for the detection of genomes of enteric viruses from water using two-step procedures: membrane filtration and RT-PCR detection. However, these methods, when applied to bottled water, generally consider only the aqueous phase. Such procedures do not take into account the adhesion of viruses onto the hydrophobic container. Potential adhesion results in loss of viral concentration in the aqueous phase and consequently viral pollution is underestimated in such a system. A procedure based on the addition of surfactant to elute viruses followed by membrane concentration was developed to avoid this underestimation. Firstly, using poliovirus 1 as a model, this study demonstrated that the best solution to recover virus and/or viral genome is a mix of sodium dodecyl sulphate, a nonionic detergent and guanidine thiocyanate. Furthermore, temperature has a significant but low effect on elution. A positively charged 0.2 μm inorganic membrane composed of Alumina (Anodisc, Whatman) is also the best membrane to concentrate viral material before the detection by RT-PCR. Finally, the developed protocol gives significantly higher poliovirus 1 recovery rate than a reference protocol previously described (aqueous phase concentration on Zetapore). The difference can be explained by the recovery of the viruses adsorbed onto the water container.