In recent decades, improving and expanding the application of magnetic iron oxide nanoparticles in various fields of science caused to double concerns among ecologists about the benefit or potential life-threatening effects of these chemical nanoparticles on human health and ecosystem. In this regard, the present study introduces the ecosystem modeling approach to the toxicity assessment of chemical magnetic nanoparticles (magnetite or Fe₃O₄) at the level of species sensitivity distributions (SSDs) in 5 different taxonomic groups of food chains of salt water and also in four taxonomic groups of freshwater chains was performed. The comparison of the average acute lethal concentration (ML(E)C₅₀) and mean mortality (MM) in both species organism in the food chain of aquatic ecosystems showed that a species sensitivity to Fe₃O₄ nanoparticles in aquatic marine ecosystems (MM=36.3%, and ML(E)C₅₀=692.9 mg/l) was higher than the organisms in the freshwater ecosystem (MM=33.8%, and ML(E)C₅₀=739.7 mg/l), and differences between groups was significant (P<0.05). Among the 9 different taxonomic groups, the most sensitive organism to magnetite nanoparticles was micro-algae Chlorella (M = 50%, and L(E)C₅₀=130 mg Fe₃O₄/l) and then crustaceans, barnacle (M=70%, and L(E)C₅₀=263.5 mg Fe₃O₄/l). However, as the species sensitivity to the acute toxicity of magnetite nanoparticles was evaluated low in all taxonomic groups, this nanomaterial can be classified as non-toxic materials.