Carbon quantum dots (CQDs) have high hydrophilicity, high cell permeability, and are frequently used in water-based and biorelated applications, yet studies concerning the ecological risks of CQDs in aquatic environments are largely insufficient. In the present study, the toxicity of CQDs to zebrafish ( Danio rerio), zooplankton ( Daphnia magna), and phytoplankton ( Scenedesmus obliquus) were assessed for the first time. The results indicated that CQDs (up to 200 mg/L) could be depurated by D. rerio with negligible toxicity. In comparison, CQDs induced mortality and immobility in D. magna with a 48-h EC50 value and LC50 value of 97.5 and 160.3 mg/L, respectively. In S. obliquus, CQDs inhibited photosynthesis and nutrition absorption in a dose- and time-dependent manner, and the growth of algae was also inhibited with a 96-h EC50 value of 74.8 mg/L, suggesting that S. obliquus, the lowest trophic level in this study, was most sensitive to CQDs exposure. Further investigations revealed that CQDs induced an increase in oxidative stress in algae cells and a decrease in pH value of an algae medium, indicating that oxidative stress and water acidification may be the mechanisms underlying the toxicity of CQDs to S. obliquus.