The effect of carbon and silicon nanotubes (CNTs and SiNTs) and carbon nanofibers (CNFs) to microscopic marine algae Heterosigma akashiwo was studied, using algal growth inhibition for 3 days (acute effect) and 7 days (chronic effect) as toxicity endpoints. The criterion of the toxic effect was the statistically significant reduction of the number of algal cells in the exposed samples compared to the control. Samples did not demonstrate toxic effects at doses 1 mg/l and 10 mg/l. CNTs and SiNTs samples at 100 mg/l exhibited both acute and chronic toxic effects. We assume that the main cause of cell death in these samples was related to the mechanical damage of cell integrity. CNFs at concentrations of 100 mg/l did not inhibit algal growth, but cells with irregular shapes were observed, which were not observed after exposure to CNTs and SiNTs. Nickel impurities present in CNFs samples are presumably the main cause of observed cell deformations.