Santos Harbor Metropolitan Area (SHMA) in São Paulo Coastline (Brazil) is the most important marine cargo transfer terminal in the Southern Hemisphere. In previous studies, the authors showed how this area is subject to climate changes determining, in the long run, a sea level rise and, as a consequence, a consistent impact on the global sea level rise and subsidence. In this research, a further and innovative analysis of a long-term-wave database (1957–2002) generated from a comparison between wave data modeled on a “deepwatermodel” (ERA-40Wavemodel—ECMWF) and wave data measured by a coastal buoy, over the years 1982– 1984, in SHMA littoral (São Paulo State, Brazil) was carried out. The calibration coefficients, according to angular sectors of the wave direction, were obtained by comparing the measured data with the modeled data and applying them to the original scenarios using a near-shorewavemodel (MIKE21). The analysis of the wave climate changes on the extreme storm surge wave conditions, selecting cases of Hs > 3.0 m and using that virtual database, has shown an increase in the wave significant height (Hs ) and in the wave peak period