In this study we exploit recent advances in high-resolution autonomous monitoring to investigate the impact of short-term variations in wind-induced mixing on the surface biomass and vertical distribution of buoyant and sinking phytoplankton species. An autonomous platform (the Automatic Water Quality Monitoring Station) moored in a Mediterranean reservoir provided minute-by-minute records of wind speed and the phytoplankton fluorescence during winter and summer. This information was then used here to quantify the impact of short-term changes in the weather on the vertical distribution of diatoms and cyanobacteria. Additionally, we apply an empirical model to determine the extent of entrainment of diatoms and cyanobacteria within the turbulent upper layers of the water column. During winter, the surface time series of fluorescence was positively correlated with the short-term variations in wind speed. In contrast, during the summer, fluorescence was negatively correlated with wind speed. In the latter case, turbulence overcame the flotation velocity of buoyant cyanobacteria, thus homogenizing their vertical distribution and decreasing surface biomass. In both cases, the dynamic response of surface phytoplankton biomass to short-term changes in wind stress was rapid, within the minute scale. As far as we know from the literature, this is the first study in which the interaction between wind stress and surface phytoplankton fluorescence has been quantified on such a fine temporal scale. Finally, relevance for forecasting and reservoir management is pointed out.