The dataset contains the authors’ materials on macrophyte diversity (macroscopic plants regardless of their taxonomic position) in rivers and streams of East European Russia and Western Siberia. These data were collected on 247 rivers and 32 streams in 13 administrative regions of the Russian Federation. The main portion of the data was obtained in water objects of the Vologda Region (5201 occurrences). In addition, there are data from Arkhangelsk Region (347 occurrences), Khanty-Mansi Autonomous Okrug (159), Yaroslavl Region (132), Novgorod Region (97), Kostroma Region (41), Republic of Karelia (31), Sverdlovsk Region (29), Komi Republic (28), Orenburg Region (26), Chelyabinsk Region (22), Voronezh Region (22), and Tyumen Region (18). Overall, the dataset contains materials on Plantae (6094) and Chromista (59) diversity. A total of 6153 occurrences (280 lower-rank taxa and 12 taxa identified to the genus level) are included in the dataset.