The growing production and application of carbon-based nanomaterials (CNMs) represent possible risks for aquatic systems. However, the variety of CNMs with different physical and chemical properties and different morphology complicate the understanding of their potential toxicity. This paper aims to evaluate and compare the toxic impact of the four most common CNMs, namely multiwalled carbon nanotubes (CNTs), fullerene (C60), graphene (Gr), and graphene oxide (GrO) on the marine microalgaePorphyridium purpureum. The microalgae cells were exposed to the CNMs for 96 h and measured by flow cytometry. Based on the obtained results, we determined no observed effect level (NOEL), and calculated EC10 and EC50 concentrations for growth rate inhibition, esterase activity, membrane potential, and reactive oxygen species (ROS) generation changes for each tested CNM. According to the sensitivity (growth rate inhibition) ofP. purpureum, the used CNMs can be listed in the following order (EC50 in mg/L, 96 h): CNTs (2.08) > GrO (23.37) > Gr (94.88) > C60 (>131.0). The toxicity of CNTs was significantly higher than the toxic effect of the other used CNMs, and only this sample caused an increase in ROS generation in microalgae cells. This effect was apparently caused by the high affinity between particles and microalgae associated with the presence of exopolysaccharide coverage onP. purpureumcells.