Coastal areas are densely populated areas, and they have been experiencing increasing pressures as a consequence of population growth, but also because of climate change aggravation. For this reason, hazard, vulnerability, and risk indexes have been becoming more recurrent, especially to study and analyze low-lying coastal areas. This study presents an analysis on wave overtopping and coastal flooding, using an Analytic Hierarchy Process (AHP) multicriteria methodology, in Costa da Caparica (Portugal). The definition of the different criteria, as well as their respective weighting for the overall problem and index calculation, was carried out with the help of experts in the subject. By following this methodology, and by using Geographic Information Systems (GIS), hazard, vulnerability, and risk indexes were obtained. The most hazardous areas are located closest to the sea, where the elevation is the lowest, whereas the most vulnerable areas are in neighborhoods with specific socioeconomic characteristics (high urban and economic density). Overall, around 30% of the study area displays moderate to very high risk regarding the occurrence of overtopping and flooding events. The results of this study will be helpful in decision-making processes in matters of coastal zone management and monitoring.