Polar shallow marginal seas are of high importance as they are the most productive regions of the Arctic Ocean and serve as filters for terrestrial runoff. Salinity and turbidity gradients create diverse habitats for planktonic organisms in coastal areas. In the present study we aimed at assessing the degree to which environmental gradients influence the abundance and community structure of the zooplankton in a shallow Arctic sea affected by terrestrial runoff. Zooplankton distribution was studied in a coastal zone in the southeastern part of the Barents Sea (Pechora Sea) in July 2014 and September 2016 along the archipelago that stretches from the continent towards the open sea. The ecosystem was in a spring state in July (2014) and in a summer state in September (2016). A clear positive gradient of salinity and a negative cline of turbidity were revealed, directed from the coast towards the open sea. A horizontal salinity gradient was detected in both seasons. The turbidity gradient was most pronounced during summer. Distribution of several species of marine zooplankton (e.g. Pseudocalanus spp., Temora longicornis, Microsetella norvegica) was associated with the salinity gradient. Parameters of community structure (species richness, diversity, evenness, total zooplankton abundance) correlated with turbidity while only diversity and evenness were influenced by salinity. A gradient was observed from a more diverse and less abundant zooplankton community in areas with high turbidity and low salinity towards a less diverse and more abundant community in the open sea. This heterogeneity influences higher trophic levels including commercial fishes and reflects how marginal filters function.