The data article refers to the paper "Distribution and grazing of the dominant mesozooplankton species in the Yenisei estuary and adjacent shelf in early summer (July 2016)" (Drits et al., 2020). The data were collected along quasi-longitudinal transect "Yenisei estuary - Kara Sea shelf" on 24-28 July 2016. Here we present data on the spatial and vertical distribution, demographic structure and gut pigment content of the dominant zooplankton species as well as the grazing impact on autotrophic phytoplankton in the three distinguished zones: freshwater zone, frontal zone of the Yenisei plume and marine shelf zone. The related article (Drits et al., 2020) considers the structure and functioning of zooplankton community in relation to environmental characteristics such as temperature, salinity, phytoplankton abundance, timing of ice retreat. Information presented in this article can be used by marine biologists for studies of structure and functioning of estuarine pelagic communities, ecology of zooplankton in the Siberian seas. Besides the data could provide a baseline for the assessment of the ecological role played by climate change events (e.g., increased precipitation, permafrost thawing, elevated river discharge) on the Arctic ecosystems.