Photoacclimation of Scenedesmus protuberans Fritsch and Microcystis aeruginosa Kutzing emend. Elenkin to high and fluctuating PPFD was studied in continuous cultures with computer-controlled variable light regimes. The aim of the work was to provide a better understanding of species-specific acclimation to high PPFD (as encountered by cyanobacteria in surface waterblooms), and of suppression of the growth of colony-forming cyanobacteria during periods of prolonged mixing in lakes. The dynamics of a set of variables was followed during the light period, including pigment composition, maximum rate, efficiency and minimum quantum requirement of photosynthesis, PS II cross-sections, and fluorescence variables. Both the green alga and the cyanobacterium displayed strong photo-inhibition of photosynthesis in the sinusoidal light regime, which simulated a natural light regime in the absence of mixing. P-max, alpha, QR and the ratio of variable to maximum fluorescence declined, and the number of inactive PS II centres and PS IIbeta centres increased towards midday. Introduction of oscillations in the diurnal light regime, simulating different intensities of wind-induced mixing in lakes, mitigated photo-inhibition. Microcystis showed a prompt non-photochemical quenching of fluorescence in all light regimes, even at low to moderate PPFD. The sustained presence of zeaxanthin in Microcystis possibly induced instant, thermal dissipation of excitation energy from the antenna. Microcystis also exhibited a more reluctant acclimation to fluctuating PPFD. Growth rate of Scenedesmus was higher in all light regimes. This implied that if (known) differences in loss processes were ignored, Scenedesmus would outcompete Microcystis in lakes. The results underlined the importance of buoyancy regulation in increasing the daily light dose of cyanobacteria (but at the same time preventing over-excitation), and ultimately in the success in Microcystis in stable lakes.