A ¹⁵N labeling technique was used to study nitrogen transfer from cyanobacterium Microcystis aeruginosa to water hyacinth. 15N atom abundance in M. aeruginosa peaked (15.52%) after cultivation in 15N-labeled medium for 3 weeks. Over 87% of algal nitrogen was transferred into water hyacinth after the 4-week co-cultivation period. The nitrogen quickly super-accumulated in the water hyacinth roots, and the labeled nitrogen was re-distributed to different organs (i.e., roots, stalks, and leaves). This study provides a new strategy for further research on cyanobacterial bloom control, nitrogen migration, and nitrogen cycle in eutrophic waters.