On the basis of summarizing the concentration distribution of typical nanomaterials in sewage treatment system and natural water body at present, the toxic effects of metal nanomaterials on microbial aggregates in sewage treatment systems(activated sludge and biofilm)and natural aquatic ecosystems(natural biofilm)were analyzed. It is proposed to study the effects of metal nanomaterials on the structure and functional characteristics of microbial communities in natural biofilms. An analysis of the negative effects on natural aquatic ecosystem by long-term exposure to low concentration was made, providing theoretical basis for pollution prevention and control of nano-materials.