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This paper addresses the effects of estimated climate change on the sea-surface dynamics of the Aegean and Ionian Seas (AIS). The main aim is the identification of climate change impacts on the severity and frequency of extreme storm surges and waves in areas of the AIS prone to flooding. An attempt is made to define design levels for future research on coastal protection in Greece. Extreme value analysis is implemented through a nonstationary generalized extreme value distribution function, incorporating time harmonics in its parameters, by means of statistically defined criteria. A 50-year time span analysis is adopted and changes of means and extremes are determined. A Regional Climate Model (RegCM3) is implemented with dynamical downscaling, forced by ECHAM5 fields under 20C3M historical data for the twentieth century and the SRES-A1B scenario for the twenty-first century. Storm surge and wave models (GreCSSM and SWAN, respectively) are used for marine climate simulations. Comparisons of model results with reanalysis and field data of atmospheric and hydrodynamic characteristics, respectively, are in good agreement. Our findings indicate that the dynamically downscaled RegCM3 simulation adequately reproduces the present general circulation patterns over the Mediterranean and Greece. Future changes in sea level pressure and mean wind fields are estimated to be small, yet significant for marine extremes. In general, we estimate a projected intensification of severe wave and storm surge events during the first half of the twenty-first century and a subsequent storminess attenuation leading to the resettlement of milder extreme marine events with increased prediction uncertainty in the second half of the twenty-first century. [ABSTRACT FROM AUTHOR]