We studied biogeochemical characteristics, including organic carbon and nitrogen contents, fatty acid (FA) composition, stable isotope ratios, and primary production in conjunction with species composition of bacterioplankton, using next generation sequencing, in the Yenisei River along a distance ∼1800 km. Basing on FA composition of particulate organic matter (POM) and on other indicators of sources of POM, the river was subdivided into four sections. The upper section 1, situated in mountain region, was the net source of high‐quality autochthonous organic matter, produced primarily by diatoms and partly consumed by specialized bacteria species. Section 2 in plain taiga was net sink of high quality allochthonous and autochthonous organic matter, produced by cyanobacteria and green algae. Section 3 was net sink of organic matter, primarily allochthonous, consumed by the specialized species of bacteria. The lowest section 4, situated in tundra, was primarily the conduit of recalcitrant terrestrial organic matter, but also the net source of autochthonous organic matter, produced by diatoms. Biogeochemical traits of sections of the Yenisei River evidently shaped dominant species composition of bacterioplankton of these sections. Regarding the biogeochemical and microbiological data, we concluded that the Yenisei River ecosystem complexly combines features of river mosaic, river continuum, and “neutral pipe.”