Feeding of dominant mesozooplankton species was investigated in freshwater zone, estuarine frontal zone of Yenisei Estuary and adjacent inner shelf area during autumn season. Ingestion rate was estimated based on gut fluorescence measurements. It was shown that in spite on the end of productive season daily ingestion of phytoplankton for the most of the investigated freshwater, brackish and marine zooplankton species was higher than their metabolic requirements. Total phytoplankton consumption by zooplankton differed in different zones. In freshwater zone under high level of autotrophic phytoplankton biomass and primary production zooplankton grazing impact was low: 1.5% of standing stock and 20% of primary production. In the estuarine frontal zone 3.2–14.3% of standing stock and 150–290% of primary production was grazed by zooplankton per day, in adjacent inner shelf: 1.4–7.0% and 130%, accordingly. Based on comparatively analysis of obtained data and results of investigation of zooplankton feeding in Ob Estuary during the same season some general patterns of the zooplankton role in organic matter biotransformation in the large arctic rivers estuarine areas were revealed.