In view of the final destination of nanomaterials, the water system would be an important sink. However, the environmental behavior of nanomaterials is rather confusing due to the complexity of the real environment. In this study, a freshwater ecosystem, including water, sediment, water lettuce, water silk, Asian clams, snails, water fleas, Japanese medaka, and Yamato shrimp, was constructed to study the distribution, bioaccumulation, and potential impacts of CeO2 nanoparticles (CeO2 NPs) via long-term exposure. The results demonstrated most of the CeO2 NPs deposited in the sediment (88.7%) when the partition approached to the constant 30 days later. The bioaccumulated Ce in six tested biota species was negatively correlated with its trophic level, showing no biomagnification of CeO2 NPs through this food web. CeO2 NP exposure induced visual abnormalities in hydrophytes, including chlorophyll loss in water silk and water lettuce, ultrastructural changes in pyrenoids of water silk, and root elongation in water lettuce. The generation of hydroxyl radical (·OH) and cell-wall loosening induced by CeO2 NP exposure might mediate the root growth in water lettuce. The findings on the environmental behavior of CeO2 NPs in water system have provided useful information on the risk assessment of nanomaterials.