In this research we present a modelling study of storm surges influenced by pre‐existing seiches in the Adriatic Sea. The natural oscillation modes – seiches – of the Adriatic Sea can be easily excited by wind, due to the particular marine bathymetry and coastal orography. Moreover, such oscillations can interact with newer wind‐induced storm surges or with other sea‐level components. This paper first considers modelling issues in the seiche reproduction, using a simplified approach, and then analyses the reproduction with the model of two extreme storm surge events, influenced by pre‐existing seiches. In order to investigate the impact of assimilating sea level data, these events are simulated without and with a data assimilation system, based on an Ensemble Kalman Filter. Results show that, while the formulation of the bottom shear stress does not influence the seiche period, the seiche decay time is correctly estimated with a hybrid linear‐quadratic formulation. We found also that non‐linear interactions of bottom currents, caused by different sea level components, can modify the decay time. However, the two events are poorly reproduced by the model, even with a correct modelling set‐up, because of wind deficiencies. Therefore we considered the issue and found that the assimilation of tide‐gauge residual sea level has a strong positive impact, lasting several days, despite the errors in the atmospheric forcing. This is mainly due to the persistence of the seiche oscillations in the Adriatic Sea.