In the present work, a methodological framework, based on nonstationary extreme value analysis of nearshore sea-state parameters, is proposed for the identification of climate change impacts on coastal zone and port defense structures. The applications refer to the estimation of coastal hazards on characteristic Mediterranean microtidal littoral zones and the calculation of failure probabilities of typical rubble mound breakwaters in Greek ports. The proposed methodology hinges on the extraction of extreme wave characteristics and sea levels due to storm events affecting the coast, a nonstationary extreme value analysis of sea-state parameters and coastal responses using moving time windows, a fitting of parametric trends to nonstationary parameter estimates of the extreme value models, and an assessment of nonstationary failure probabilities on engineered port protection. The analysis includes estimation of extreme total water level (TWL) on several Greek coasts to approximate the projected coastal flooding hazard under climate change conditions in the 21st century. The TWL calculation considers the wave characteristics, sea level height due to storm surges, mean sea level (MSL) rise, and astronomical tidal ranges of the study areas. Moreover, the failure probabilities of a typical coastal defense structure are assessed for several failure mechanisms, considering variations in MSL, extreme wave climates, and storm surges in the vicinity of ports, within the framework of reliability analysis based on the nonstationary generalized extreme value (GEV) distribution. The methodology supports the investigation of future safety levels and possible periods of increased vulnerability of the studied structure to different ultimate limit states under extreme marine weather conditions associated with climate change, aiming at the development of appropriate upgrading solutions. The analysis suggests that the assumption of stationarity might underestimate the total failure probability of coastal structures under future extreme marine conditions.