We propose a dynamic model specifically designed to simulate changes in the photosynthetic electron transport rate, which is calculated from fluorescence measurements when plants are exposed, for a short time, to a series of increasing photon flux densities. This model simulates the dynamics of the effective yield of photochemical energy conversion from the maximum and natural chlorophyll fluorescence yields, taking into account a cumulative effect of successive irradiations on photosystems. To estimate a characteristic time of this effect on photosystems, two series of experiments were performed on two benthic diatom culture concentrations. For each concentration, two different series of irradiations were applied. Simplified formulations of the model were established based on the observed fluorescence curves. The simplified versions of the model streamlined the parameters estimation procedure. For the most simplified version of the model (only 4 parameters) the order of magnitude of the characteristic time of the residual effect of irradiation was about 38 s (within a confidence interval between 20 and 252 s). The model and an appropriate calibration procedure may be used to assess the physiological condition of plants experiencing short time-scale irradiance changes in experimental or field conditions.