Nanoparticles (NPs) have broad applications in medicine, cosmetics, optics, catalysis, environmental purification, and other areas nowadays. With increasing annual production of NPs, the risks of their harmful influence on the environment and human health are also increasing. Currently, our knowledge about the mechanisms of the interaction between NPs and living organisms is limited. The marine species and their habitat environment are under continuous stress owing to the anthropogenic activities, which result in the release of NPs in the aquatic environment. We used a bioassay model with hemocytes of three bivalve mollusc species, namely, , , and , to evaluate the toxicity of 10 different types of NPs. Specifically, we compared the cytotoxic effects and cell-membrane polarization changes in the hemocytes exposed to carbon nanotubes, carbon nanofibers, silicon nanotubes, cadmium and zinc sulfides, Au-NPs, and TiO NPs. Viability and the changes in hemocyte membrane polarization were measured by the flow cytometry method. The highest aquatic toxicity was registered for metal-based NPs, which caused cytotoxicity to the hemocytes of all the studied bivalve species. Our results also highlighted different sensitivities of the used tested mollusc species to specific NPs.