A 3D hydrodynamic model has been applied to the Curonian Lagoon to study the pollution impact of E. coli on a new beach that might be opened in the lagoon. Through a field survey the E. coli inputs were measured and then used in the numerical model, and through laboratory experiments the decay rate of E. coli was established. The model has been calibrated and validated for the year 2015, and several scenarios have been studied, such as sewage system breakdown, severe weather conditions or high river loads. The model has then been run for a period of 12 years to obtain a robust statistics for the pollution on the planned beach. Results show that the decay rate of E. coli is between 0.55 days and 2.3 days and the modeled decay times are compatible with these numbers. The only scenario that would create a risk for the bathing waters of the beach is a breakdown of the sewage system on the Curonian Spit. In this case the hours (and days) over legally allowable bathing threshold were computed in order to estimate the number of days the beach could be closed. These results have been confirmed by the 12 year simulations. With an influence map analysis the two most critical sewage systems could be identified.