Microalgae are key organisms in aquatic ecosystems. Emergent pollutants like the tetrabromobisphenol A (TBBPA) are potential threat for these primary producers at the base of the trophic chain. The effects of this flame retardant on three microalgae (Pseudokirchneriella subcapitata, Nitzschia palea and Chlamydomonas reinhardtii) commonly observed in freshwater ecosystems were studied using a flow cytometer. Each species was exposed to 1.8, 4.8, 9.2, 12.9 and 16.5 µmol L−1 of TBBPA for 72 h. After staining with fluorescein diacetate (FDA), viable cells were discriminated in flow cytogram according to the chlorophyll autofluorescence and the intracellular enzyme activity (esterase) to assess the sensitivity of microalgae to the TBBPA with multi-parametric analysis. For P. subcapitata and N. palea, growth inhibitions of viable cells were lower when the viability was assessed with chlorophyll autofluorescence in comparison with esterase activity. These results are related to the appearance of cells presenting optimal chlorophyll fluorescence without intracellular esterase activity after exposure to TBBPA. Abundance increase of these cells was higher in N. palea than in P. subcapitata. No similar trends were observed in C. reinhardtii populations due to the very high mortality of this microalgal species exposed to TBBPA.