Rivers, lakes and the sea were the natural receivers of raw urban waste and storm waters for a long time but the low sustainability of such practice, the increase of population and a renewed environmental sensibility increased researcher interest in the analysis and mitigation of the impact of urban waters on receiving water bodies (RWB). In Europe, the integrated modelling of drainage systems and RWB has been promoted as a promising approach for implementing the Water Framework Directive. A particular interest is given to the fate of pathogens and especially of Escherichia coli, in all the cases in which an interaction between population and the RWB is foreseen. The present paper aims to propose an integrated water quality model involving the analysis of several sewer systems (SS) discharging their polluting overflows on the coast in a sensitive marine environment. From a modelling point of view, the proposed application integrated one-dimensional drainage system models with a complex three-dimensional model analysing the propagation in space and time of E. coli in the coastal marine area. The integrated approach was tested in a real case study (the Acicastello bay in Italy) where data were available both for SS model and for RWB propagation model calibration. The analysis shows a good agreement between the model and monitored data. The integrated model was demonstrated to be a valuable tool for investigating the pollutant propagation and to highlight the most impacted areas.