Fullerenol, a water-soluble polyhydroxylated fullerene nanomaterial, enters aquatic organisms and ecosystems through different ingestion exposures and may pose environmental risks. The study of their uptake routes and transfer in aquatic systems is scarce. Herein, we quantitatively investigated the aquatic uptake and transfer of 13C-fullerenols from Scenedesmus obliquus to Daphnia magna using 13C-skeleton-labeling techniques. The bioaccumulation and depuration of fullerenol in Daphnia magna increased with exposure doses and time, reaching steady state within 16 h in aqueous and feeding-affected aqueous routes. The capacity of Daphnia magna to ingest fullerenol via the aqueous route was much higher than that via the dietary route. From the aqueous to feeding-affected aqueous, the kinetic analysis demonstrated the bioaccumulation factors decreases, which revealed that algae suppressed Daphnia magna uptake of fullerenols. The aqueous route was the primary fullerenols ingestion pathway for Daphnia magna. Kinetic analysis of the accumulation and transfer in Daphnia magna via the dietary route indicated low transfer efficiency of fullerenol along the Scenedesmus obliquus-Daphnia magna food chain. Using stable isotope labeling techniques, these quantitative data revealed that carbon nanomaterials underwent complex aquatic accumulation and transfer from primary producers to secondary consumers and algae inhibited their transfer in food chains.