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The Pacific island countries are particularly vulnerable to the effects of global warming including more frequent and intense natural disasters. Seawater inundation, one of the most serious disasters, could damage human property and life. Regional sea level rise, highest astronomic tide, vertical land motions, and extreme sea level could result in episodic, recurrent, or permanent coastal inundation. Therefore, assessing potential flooding areas is a critical task for coastal management plans. In this study, a simulation of the static flooding situation in the southwest coast of Taiwan (Tainan city) at the end of this century was conducted by using a combination of the Taiwan Digital Elevation Model (DEM), regional sea level changes reconstructed by tide gauge and altimetry data, vertical land deformation derived from leveling and GPS data, and ocean tide models. In addition, the extreme sea level situation, which typically results from high water on a spring tide and a storm surge, was also evaluated by the joint probability method using tide gauge records. To analyze the possible static flood risk and avoid overestimation of inundation areas, a region-based image segmentation method was employed in the estimated future topographic data to generate the flood risk map. In addition, an extreme sea level situation, which typically results from high water on a spring tide and a storm surge, was also evaluated by the joint probability method using tide gauge records. Results showed that the range of inundation depth around the Tainan area is 0–8 m with a mean value of 4 m. In addition, most of the inundation areas are agricultural land use (60% of total inundation area of Tainan), and two important international wetlands, 88.5% of Zengwun Estuary Wetlands and 99.5% of Sihcao Wetlands (the important Black-faced Spoonbills Refuge) will disappear under the combined situation. The risk assessment of flooding areas is potentially useful for coastal ocean and land management to develop appropriate adaptation policies for preventing disasters resulting from global climate change. Full article