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In photosynthetic microorganisms, the toxicity of carbon nanomaterials (CNMs) is typically characterized by a decrease in growth, viability, photosynthesis, as well as the induction of oxidative stress. However, it is currently unclear how the shape of the carbon structure in CNMs, such as in the 1-dimensional carbon nanotubes (CNTs) compared to the two-dimensional graphene oxide (GO), affects the way they interact with cells. In this study, the effects of GO and oxidized multi-walled CNTs were compared in the cyanobacterium Microcystis aeruginosa to determine the similarities or differences in how the two CNMs interact with and induce toxicity to cyanobacteria. Using change in Chlorophyll a concentrations, the effective concentrations inducing 50% inhibition (EC50) at 96 h are found to be 11.1 μg/mL and 7.38 μg/mL for GO and CNTs, respectively. The EC50 of the two CNMs were not found to be statistically different. Changes in fluorescein diacetate and 2′,7′-dichlorodihydrofluorescein diacetate fluorescence, measured at the EC50 concentrations, suggest a decrease in esterase enzyme activity but no oxidative stress. Scanning and transmission electron microscopy imaging did not show extensive membrane damage in cells exposed to GO or CNTs. Altogether, the decrease in metabolic activity and photosynthetic activity without oxidative stress or membrane damage support the hypothesis that both GO and CNTs induced indirect toxicity through physical mechanisms associated with light shading and cell aggregation. This indirect toxicity explains why the intrinsic differences in shape, size, and surface properties between CNTs and GO did not result in differences in how they induce toxicity to cyanobacteria.