Manufactured nanomaterials have been widely used in life because of their unique physical and chemical properties. The environmental behaviors and biological safety of manufactured nanomaterials in water had become a hotspot in research of environmental science. The effects of manufactured nanomaterials in water-biofilm system and its influencing mechanisms are the key scientific problems, which are urgent to be solved. This review discusses the toxicity effects of nanomaterials on aquatic organisms, which cause bacterial death, inhibiting the growth of algae. The main influences of manufactured nanomaterials on biofilms are bacterial activity, microbial community structure, net pollution activity, and related key enzyme activity. The toxicity mechanism of nanomaterials can be investigated adsorption on biofilms or penetrate into the cell membrane, lead to the DNA damage, lipid peroxidation, protein modifications and oxidative stress of the bacteria biofilms by producing excess reactive oxygen species. Also, the adsorption mechanism of biofilm for nanomaterials was discussed, and illustrates the adsorption of biofilm on nanomaterials is the most important ways of its removal from water. The results of this review provide an important theoretical basis on further study the mechanism of interacation between nanomaterials and biofilms.