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Microbiological impact is critical in coastal areas where tourism is particularly important for both the local and regional economy. Submarine outfalls are commonly used to enhance the dispersion of treated sewage thus avoiding pollution along the coast. The Venice lagoon (North Italy) has a very sensitive ecosystem, due to the morphological and natural characteristics of the basin and the co-existence of human activities. To preserve the lagoon, the discharge from the treatment plant for urban wastewater collected from the Venezia-Mestre agglomeration, neighbouring areas and local industries (total of 400,000 population equivalent-PE) has been moved from the lagoon to the open Adriatic Sea since November 2013 by means of an approximately 20-km pipeline. Microbiological pollution inside the lagoon can affect shellfish breeding areas instead, along the coast it affects the quality of bathing waters. In this study, and for the first time, a 3D hydrodynamic SHYFEM model (shallow water finite element model) with high spatial resolution coupled with a microbiological module has been applied to the lagoon and to the Adriatic Sea, to evaluate the effectiveness of the location of the submarine outfall. Microbiological data have been produced by the control Authority according to official analytic methods and by the plant operator. The module of survival of free Escherichia coli follows a variable rate in dependence of UV radiation, temperature and salinity in the water. Two scenarios were modelled: final discharge into the lagoon before November 2013 and after into the open sea. In the latter case, two situations have been considered, one with "Bora" and the other with "Scirocco" winds. Our results indicate that the model correctly simulates microbiological decay and dispersion. The transferral of the final discharge point far from the shoreline improves pollution dispersion, thus preserving the lagoon without evidence of impacts on the bathing waters in all meteorological conditions.