The effect of the herbicide paraquat on the freshwater microalga Chlamydomonas eugametos was studied in function of different parameters such as growth, elemental composition, total lipids, and photosynthetic pigments content and others assayed by flow cytometry (cell viability, cell volume, and granularity). The study reveals that paraquat concentrations above 0.15 microM are toxic for the microalga C. eugametos, inducing an inhibition of all the physiological parameters analyzed and strong structural changes. However, lower concentrations cause alterations in certain cellular components that are especially sensitive to the toxic action of the herbicide; so total lipids and photosynthetic pigments content are affected by concentrations such low as 0.037 microM. Taking into account these results, these parameters are better indicators of the cellular state than data on biomass or growth rate.