Bacterial pathogens in coastal aquatic ecosystems pose a potential public health hazard for bathing water use. The European Bathing Water Directive (2006/7/EC) currently relies on the culturability of fecal pollution bacterial indicators such as Escherichia coli, without considering dormant or quiescent (Viable But Not Culturable, VBNC) cells, whose possible resuscitation after bathers ingestion cannot be excluded. Standard methods are also time-consuming and therefore hardly meet early warning needs of marine monitoring. To solve this issue, a new index, the Bathing Water Quality Index (BWQI), has here been developed, allowing to identify the most favorable coastal zones for recreational use. The index was calculated by combining numerical simulations of living and dormant E. coli abundances and their residence times. To specifically set up the model with the different physiological states of the whole E. coli population, an ad hoc experiment based on the fluorescent antibody method was performed. The BWQI application to Santa Marinella bathing area highlights a potential risk for human health in the zone most frequented by bathers. This study provides a predictive tool to support preventive decisions of the competent authorities and to properly protect bathers’ health, stressing the need for improved methods for environmental monitoring.