Due to their remarkable properties, the applications of carbon-based nanomaterials (CNMs) such as graphene and functionalized multi-walled carbon nanotubes (f-MWCNTs) are increasing. These CNMs can enter the freshwater environment via numerous routes, potentially exposing various organisms. The current study assesses the effects of graphene, f-MWCNTs, and their binary mixture on the freshwater algal species Scenedesmus obliquus. The concentration for the individual materials was kept at 1 mg L−1, while graphene and f-MWCNTs were taken at 0.5 mg L−1 each for the combination. Both the CNMs caused a decrease in cell viability, esterase activity, and photosynthetic efficiency in the cells. The cytotoxic effects were accompanied by increased hydroxyl and superoxide radical generation, lipid peroxidation, antioxidant enzyme activity (catalase and superoxide dismutase), and mitochondrial membrane potential. Graphene was more toxic compared to f-MWCNTs. The binary mixture of the pollutants demonstrated a synergistic enhancement of the toxic potential. Oxidative stress generation played a critical role in toxicity responses, as noted by a strong correlation between the physiological parameters and the biomarkers of oxidative stress. The outcomes from this study emphasize the significance of considering the combined effects of various CNMs as part of a thorough evaluation of ecotoxicity in freshwater organisms.