Effects of wind and waves on the surface dynamics of the Mediterranean Sea are assessed using a modified Ekman model including a Stokes-Coriolis force in the momentum equation. Using 25 years of observations, we documented intermittent but recurrent episodes during which Ekman and Stokes currents substantially modulate the total mesoscale dynamics by two non-exclusive mechanisms: (i) by providing a vigorous input of momentum (e.g. where regional winds are stronger) and/or (ii) by opposing forces to the main direction of the geostrophic component. To properly characterize the occurrence and variability of these dynamical regimes we perform an objective classification combining self-organizing maps (SOM) and wavelet coherence analyses. It allows proposing a new regional classification of the Mediterranean Sea based on the respective contributions of wind, wave and geostrophic components to the total mesoscale surface dynamics. We found that the effects of wind and waves are more prominent in the northwestern Mediterranean, while the southwestern and eastern basins are mainly dominated by the geostrophic component. The resulting temporal variability patterns show a strong seasonal signal and cycles of 5 - 6 years in the total kinetic energy arising from both geostrophic and ageostrophic components. Moreover, the whole basin, specially the regions characterized by strong wind- and wave- induced currents, shows a characteristic period of variability at $5$ years. That can be related with climate modes of variability. Regional trends in the geostrophic and ageostrophic currents shows an intensification of 0.058 +-1.43 10^-5 cm/s per year.