With the rapid development of nanotechnology industry, there is an increased discharge of engineered nano-particles (ENPs) into aquatic environments; therefore, the study of their ecotoxicity and environmental risk is urgently required. This paper reviews the toxicological mechanisms of ENPs and the filter of model organisms. Researchers have pointed out two main traits of nanoparticle cytotoxicity:affection of cell signaling pathways and reactive oxygen species (ROS)-related changes in gene expression. Oxidative stress caused by ROS production inside cells can change the levels of anti-oxidative enzymes, and then destroy the balance between oxidation and anti-oxidation. Thus, cells are damaged by ROS accumulation, leading to a series of consequences, such as lipid oxidation and inhibited cell growth. Previous studies have suggested that photosensitivity of ENPs and their ROS production under high-intensity light with specific wavelengths may be related to their ENP toxicity. The adsorption of ENPs on the surface of microorganisms or cells can hinder their normal physiological functions; in addition, the adsorption of ENPs can also enhance the absorption of hazardous substances in microorganisms or cells. Since the toxicity testing conditions of ENPs may vary, and there is no uniform requirement for solvent type and use; therefore, toxicity research of ENPs is not based on the same principles. In the ecotoxicological assessment of ENPs, the effects of solvents should be taken into consideration, and it is necessary to assess whether other substances will produce toxicity under the influence of ENPs. In addition, solubility, surface characteristics, forms of metal oxides are also important toxicological mechanisms of ENPs. In nano-ecological toxicology studies, the filter and determination of optimal model organisms is vital. It has been widely demonstrated and recommended that fish should be considered as a primary model animal for the evaluation of the potential acute aquatic toxicity of ENPs. Fish are the most dominant vertebrates in the aquatic environments. Fish demonstrate high sensitivity of behavior endpoint and obvious concentration-response relationship in bio-toxicity experiments. Therefore, fish are considered to be the most suitable model organism in aquatic ecotoxicological research. A few studies have shown that behavioral endpoints of developing fish are more effective in detecting toxicity of ENPs compared to traditional studies such as embryonic development and fatality rate. It is emphasized that in ecotoxicological research of ENPs, further aquatic invertebrate testing will be of great significance, particularly studies on bioaccumulation and chronic endpoints with long-term low exposure. Bivalves represent an ideal group for studying the effects of ENPs, since they are abundant in both freshwater and marine aquatic environments. In addition, phytoplankton are important producers in aquatic environments, occupying an important place in aquatic ecosystems. Toxic effects of ENPs to phytoplankton and saving of ENPs by phytoplankton can directly or indirectly affect the entire aquatic ecosystem. Invertebrates and phytoplankton are both dominant in aquatic environments, and are highly sensitive to pollutants; they have significant enrichment and amplification effect on harmful substances. Therefore, they also have a certain advantage as model organisms.