The frequent detection of polychlorinated diphenyl ethers (PCDEs) in aquatic systems has aroused widespread concerns, however, their potential hazard to aquatic ecosystems has been poorly understood. Here the acute toxicity of 12 PCDE congeners was evaluated in three model aquatic organisms representing different trophic levels following OECD test guidelines, including green algae (Scenedesmus obliquus), water flea (Daphnia magna), and zebrafish (Danio rerio). Dose-dependent increases in growth inhibition and mortality were observed for all tested PCDE congeners. Most of the PCDE congeners, in particular 3,3',4,4'-tetra-CDE, were highly toxic to the three aquatic organisms with EC50 or LC50 values below 1 mg L-1. Their toxicities were generally comparable with those of certain polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs). Moreover, D. magna was the most sensitive species among the three aquatic organisms. In addition, the EC50 or LC50 values had an extremely significant correlation with the n-octanol-water partition coefficient (logKow) of the PCDE congeners. The established quantitative structure-property relationship (QSPR) models indicated that the molecular polarizability (α) could significantly influence the acute toxicity of PCDEs on Daphnia magna and Danio rerio, and the energy of the lowest unoccupied molecular orbital (ELUMO) is the key factor of the acute toxicity of PCDEs in Scenedesmus obliquus. In addition, even at environmental levels, 3,3',4,4'-tetra-CDE could induced seveve oxidative damages in the three aquactic species. These findings would contribute to the understanding of adverse effects of PCDEs in aquatic organisms.