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Low-elevation coastal areas and their populations are at risk during and after the appearance of a storm surge event. Coastal flooding as a result of storm surge events is investigated in this paper for a number of areas around the north-eastern (NE) Mediterranean coastal zone (Adriatic, Aegean and north Levantine seas). The sea level rise (SLR) due to storm surge events is examined for the period 2000–2004. Wind data, atmospheric pressure and wave data for this period as well as in situ sea elevation measurements (from stations around the Mediterranean coasts) were used. Potential inundation zones were then identified using a 90-m horizontal resolution digital elevation model (DEM). At these zones, the sea surface elevations were calculated for the study period, using the collected data and a 2D storm surge simulation model (1/10o×1/10o) output, examining the sea level alteration in specific coastal areas, where in situ measurements are absent and are characterised as “risky” in inundation areas, due to their topography. In order to determine the level of storm track implication on major SLR incidents, the trajectories of the respective storm events were computed. The aim of this paper is to investigate the major storm surge events that appeared during the study period, identify the major “risky” costal regions along the north-eastern Mediterranean coast and determine their hazard level due to inundation caused by storm surge phenomena. The combination of the risk level determination of an area and the calculation of sea level alteration is an important tool in terms of predicting and protecting the coastal area from extreme meteorological incidents.