The enantioselective environmental behaviors of the chiral insecticide fipronil and its metabolites in lab-scale aquatic ecosystems were studied and the toxicity of fipronil enantiomers and the metabolites to non-target organisms Lemna minor (L. minor) and Anodonta woodiana (A. woodiana) was also investigated in this work. Water-sediment, water-L. minor, water-A. woodiana, and water-sediment-L. minor-A. woodiana ecosystems were set up and exposed to fipronil through a 90-day period. The results showed fipronil could be degraded significantly faster (half-life of 4.6 days) in the complex water-sediment-L. minor-A. woodiana ecosystem. A. woodiana played a crucial role in the dissipation of fipronil, and the microorganisms in the sediment also made great contribution to the degradation of fipronil in aquatic ecosystems. All the three metabolites fipronil desulfinyl, fipronil sulfide and fipronil sulfone were detected in the ecosystems and were more persistent than fipronil. Enantioselective degradation of fipronil was observed with S-fipronil being preferentially degraded in sediment and L. minor, while R-fipronil was metabolized preferentially in A. woodiana. EC50 for L. minor was obtained using 7-day exposure, and for A. woodiana was obtained using 72-h exposure. S-fipronil was more toxic to A. woodiana, while R-fipronil showed higher toxicity to L. minor. Moreover, the three metabolites were found more toxic than fipronil indicating significant environment risks due to their persistence. The present study might have important implications for the risk assessment of fipronil and its metabolites in real aquatic environment.