This work is related to the environmental toxicology risk assessment and evaluation of the possible transformation of carbon-based nanomaterials (CNMs) after contact with marine microalgae. The materials used in the study represent common and widely applied multi-walled carbon nanotubes (CNTs), fullerene (C60), graphene (Gr), and graphene oxide (GrO). The toxicity was evaluated as growth rate inhibition, esterase activity, membrane potential, and reactive oxygen species generation changes. The measurement was performed with flow cytometry after 3, 24, 96 h, and 7 days. The biotransformation of nanomaterials was evaluated after 7 days of microalgae cultivation with CNMs by FTIR and Raman spectroscopy. The calculated toxic level (EC50in mg/L, 96 h) of used CNMs reduced in the following order: CNTs (18.98) > GrO (76.77) > Gr (159.40) > C60(414.0). Oxidative stress and membrane depolarization were the main toxic action of CNTs and GrO. At the same time, Gr and C60decreased the toxic action with time and had no negative impact on microalgae after 7 days of exposure even at the concentration of 125 mg/L. Moreover, C60and Gr after 7 days of contact with microalgae cells obtained structural deformations.