We developed a storm surge Ensemble Prediction System (EPS) for the Goro lagoon (GOLFEM-EPS) in the Northern Adriatic Sea. The lagoon is threatened every year by storm surge events with consequent risks for human life and economic losses. We show the advantages and limitations of an EPS with 45 members, using a very high-resolution unstructured grid finite element model. 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 run-off, initial and lateral boundaries are evaluated, 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.