With the rapid development of nanotechnology and widespread use of nanoproducts, ecotoxicity of engineered nanoparticles (NPs) attracts increasing attention and research. This paper reviews the ecotoxicity and mechanisms of NPs to aquatic organisms systematically. Toxic effects of different classes of NPs to bacteria, algae, invertebrates and fish in aquatic environments were firstly summarized, possible toxicity mechanisms were then expounded and the relationship between toxicity mechanisms and unique physicochemical properties of NPs was also analyzed. The processes of NPs uptake and membrane penetration at the cell and molecular level were discussed and presented. In the natural water, NPs behaviors are influenced by water chemistry conditions, so toxic effect to aquatic organisms is different from that in laboratory conditions, which should be paid with increased attention and effort. Finally, bottle-necks and challenges of NPs ecotoxicity research and existing problems of test and analytical methods were analyzed and the future directions of research were suggested.