a b s t r a c tMost studies on the behavior and toxicity of engineered nanoparticles (NPs) have been conducted in artificial water with well-controlled conditions, which are dramatically different from natural waters with complex compositions. To better understand the fate and toxicity of NPs in the natural water environment, physicochemical transformations of four NPs (TiO 2 , ZnO, Ag, and carbon nanotubes (CNTs)) and their toxicities towards a unicellular green alga (Chlorella pyrenoidosa) in four fresh water and one seawater sample were investigated. Results indicated that water chemistry had profound effects on aggregation, dissolution, and algal toxicity of the NPs. The strongest homoaggregation of the NPs was associated with the highest ionic strength, but no obvious correlation was observed between the homoaggregation of NPs and pH or dissolved organic matter content of the water samples. The greatest dissolution of ZnO NPs also occurred in seawater with the highest ionic strength, while the dissolution of Ag NPs varied differently from ZnO NPs. The released Zn 2þ and especially Ag þ mainly accounted for the algal toxicity of ZnO and Ag NPs, respectively. The NP-cell heteroagglomeration occurred generally for CNTs and Ag NPs, which contributed to the observed nanotoxicity. However, there was no significant correlation between the observed nanotoxicity and the type of NP or the water chemistry. It was thus concluded that the physicochemical transformations and algal toxicities of NPs in the natural water samples were caused by the combined effects of complex water quality parameters rather than any single influencing factor alone. These results will increase our knowledge on the fate and effects of NPs in the aquatic environment.