The content of rare earth elements (REE: La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu) in macrophytes and water of the Ivankovskoye reservoir was determined for the first time using a modern analytical method of inductively coupled plasma mass spectrometry (ICP-MS). REE compositions were comparatively characterized in macrophytes belonging to different ecological groups – helophytes (wetland plants) and hydrophytes (submerged plants) growing in bays with different anthropogenic load. Two macrophyte species, Glyceria aquatica (L.) Wahlb. and Potamogeton perfoliatus L., were chosen as objects for biogeochemical studies. The highest REE content was found in Potamogeton perfoliatus L. from the group of submerged plants (hydrophytes). The coefficients of biological absorption of rare earth elements (Kb) were calculated in macrophytes relative to water. It was established that in areas with high anthropogenic load, macrophytes accumulated large quantities of REE. Factor and correlation analysis of the data showed that most of the REE were associated with Fe and Al, with high positive correlation coefficients obtained in the group of submerged plants. In the group of wetland plants high positive coefficients of correlation with Fe and Al were obtained only for light REE. Coefficients of correlation with Mn were negative for both ecological groups. Thus, the processes of sorption and co-precipitation of REE on iron oxyhydroxides, as well as the formation of colloids and organic compounds associated with Fe and Al play an important role in REE migration in aquatic ecosystems. High values of coefficients of biological absorption of rare earth elements indicate their active participation in the biochemical processes in higher aquatic vegetation.