Storm surges and associated coastal flooding are among the most damaging natural disasters, as it was illustrated recently in the Gulf of Mexico, the Bay of Bengal or the Philippines. Storm surges correspond to sea-level anomalies, driven by atmospheric pressure, wind and short waves. In shallow waters, the wind contribution is usually dominant upon the other forcing, which causes coastal areas bordered by extensive shelves and located along the track of major storms to be exposed to very large surges. For a given wind speed, the surface stress can also be amplified by sea-states, for instance in the presence of young and steep waves. The Coriolis effect associated with the Earth rotation is also an important process because it deviates wind-driven flows to the right (to the left) in the Northern (Southern) hemisphere, which can result to an Ekman setup along the coast located to the right-side (resp. left-side) of the storm track. Finally, wave dissipation in surf zones induces gradients of radiation stress, which drives a wave-setup easily reaching several tens of cm and therefore contribution to the whole storm surge. Coastal flooding usually happens when a large storm surge peak at the same time of a high tide, although the importance of this concomitance depends and surge to tidal range ratio. Coastal flooding can occur through dike and barriers overflowing, breaching, or a combination of both mechanisms. Along the coastline exposed to big waves, wave overtopping can also induce significant flooding and damage sea-front. However, resolving shortwave phases to account for this phenomenon implies a very fine resolution, which poses a serious challenge in terms of computational resources.