Due to the inevitable achievement of nanoparticles to aquatic ecosystems, the limitation of existing reports, and the inadequate understanding of their possible biological reactions with aquatic organisms, this study in the pioneering step was aimed to toxicity assessment of aqueous suspension of chemical magnetic nanoparticles (Fe₃O₄) in zooplanktonic species such as barnacle larvae Amphibalanus amphitrite (sea water index) and rotifer Brachionus rotundiformis (fresh water index). For this purpose, serial concentrations (0, 10, 50, 100, 200, 500 mg / l) of magnetite nanoparticles were prepared in 24 well plates with 5 replicates. After that, the zooplanktons (50 barnacle nauplii and 20 neonate rotifer to each well) were introduced to plates and the sensitivity of the samples were evaluated for the toxicity of nanoparticles at a time interval of 12-48 hours. The results of this study showed that the toxicity effects of chemical magnetite nanoparticles on barnacle nauplii larvae and neonate rotifer were increased with increasing time and concentration of magnetite nanoparticles. Differences between control and treatment groups were significant (P<0.05). However, after 48 hours of exposure, the mortality rate at the highest concentration (500 mg/l) in barnacles was 62% (LC₅₀= 466.5 mg/l) and in rotifer 34% (E₅₀>1000 mg/l). Regardless of species variation in barnacles and rotifers, according to the results, magnetite nanoparticles are in the group of non-toxic contaminants for these zooplanktonic organisms.