Light variation in temporal and spatial domains is a key constraint on the photosynthetic performance of phytoplankton. The most obvious responses are the modification of cell pigment content either to improve photocapture or to mitigate photo-damage. Very few studies have analyzed whether light variation significantly alters carbon assimilation, especially in a fluctuating light environment as in the mixed layer of the ocean. We addressed the question using a modeling approach, which allows the reproduction of most of the possible scenarios, obtained with great difficulty from laboratory or field experiments. The complete model is based on the dynamic coupling of a photoacclimation and photodamage-repair responses. In this combined model the virtual phytoplankton is exposed to different light regimes (steady, square wave, sinusoidal light-dark cycles and fluctuating regimes). The results reconcile controversial results on different photoacclimation states achieved during fluctuating light regimes. The model produces a depression of carbon assimilation in any light fluctuating scenario, as compared to steady light regimes, due to the temporal delay between light fluctuations and photoresponses. These results suggest the possibility of selective pressure during evolution, more effective on photoprotective mechanisms than on optimization of light harvesting.