The authors provide data on the taxonomic composition, structure and quantitative characteristics of zooplankton and zoobenthos from the river mainstream, floodplain water bodies and channels in the upper reaches of Lena River. Plankton includes 84 species, among which C. scutifer scutifer, a relict species from the north inhabiting Lake Istok on Lena River.  Judging by the structure and quantitative characteristics of zooplankton, the trophic status of these waters changes from oligotrophic to α-mesotrophic. The zoobenthos is composed mainly of dragonfly larvae, mayflies, caddisflies and chironomids.