Macrozooplankton assemblages were studied during the summer and fall of 2012 in the Pechora Sea, a large coastal region of the south-eastern Barents Sea strongly affected by discharges of freshwater. Sampling was performed at 23 stations with 550-μm mesh IKS-80 nets. We focused on macrozooplankton and large (>1.5 mm) non-copepod zooplankton (larvae of benthic animals and medusae). A combination of multivariate cluster analysis, diversity indices and canonical correspondence analysis was used to relate the spatio-temporal patterns of the zooplankton assemblages to environmental factors. Summer macrozooplankton density varied from 3 to 928 ind. m−3, averaging 131 ± 49 ind. m−3, with medusae being the most numerous (mean ± SE: 67.9 ± 7.8% of the total abundance). The total macrozooplankton biomass ranged from 0.3 to 516 mg dry mass (DM) m−3 with a mean value of 28 ± 25 mgDM m−3. There was a clear decline in the total macrozooplankton abundance (1.1–6.0, 4.4 ± 1.6 ind. m−3) and biomass (0.4–2.7, 1.2 ± 0.7 mgDM m−3) in fall when only two taxa (Parasagitta elegans and Mertensia ovum) were identified. Cluster analysis revealed three groups of stations in summer. The clusters were similar in terms of the abundance in common taxa but differed by the total density, biomass and diversity. We found that the offshore zone was dominated by the euphausiids Thysanoessa spp. and the chaetognaths Parasagitta elegans while the coastal area was characterized by high density of hydromedusae and larvae of bottom animals (Hyas spp., Pagurus spp.). There was a significant decline in the total macrozooplankton abundance and biomass from summer to fall. Canonical correspondence analysis showed that during the summer and fall of 2012, 68% of macrozooplankton variability was explained by environmental factors with water temperature and longitude being the most important. The distribution of macrozooplankton taxa was also related to local circulation patterns and possibly to mesozooplankton as potential prey for carnivorous taxa. Our data may be useful for future monitoring in the coastal Arctic estuarine regions.