We developed a storm surge Ensemble Prediction System (EPS) for lagoons and transitional environments. Lagoons are often threatened by storm surge events with consequent risks for human life and economic losses. The uncertainties connected with a classic deterministic forecast are many, thus an ensemble forecast system is required to properly consider them and inform the end-user community accordingly. The technological resources now available allow to investigate the possibility of operational ensemble forecasting systems that will become increasingly essential for coastal management. We show the advantages and limitations of an EPS applied to a Lagoon, using a very high-resolution unstructured grid finite element model and 45 EPS members. For five recent storm surge events, the EPS generally improves the forecast skill on the third forecast day compared to just one deterministic forecast, while they are similar in the first two days. A weighting system is implemented to compute an improved ensemble mean. The uncertainties regarding sea level due to meteorological forcing, river runoff, initial and lateral boundaries are evaluated for a special case in the northern Adriatic Sea, and the different forecasts are used to compose the EPS members. We conclude that the largest uncertainty is in the initial and lateral boundary fields at different time and space scales, including the tidal components.