Abstract Current climate change is significantly modifying Arctic ecosystems and their components, but the reference and direction of these changes are still undefined. The aim of this study was to provide well-grounded data on the present composition and structure of zooplankton from boreal to Arctic latitudes. This comparative study was performed with a unified methodology in six fjords located along the west coasts of Norway and Svalbard. Comparisons between the fjords' environmental characteristics (temperature, salinity, chlorophyll, and particles) and the zooplankton community, described with several metrics (abundance and biovolume) and traits (taxonomy and size), were performed to recognise the potential of various ecological indicators for future monitoring. While hydrography and the taxonomic composition of zooplankton were specific to each fjord and changed along the latitudinal environmental gradient, the clustering of particle characteristics (size, concentration, and transparency) and zooplankton size structures alludes to their susceptibility to additional, local processes. The differences in the biotic and abiotic characteristics distinguished the semi-closed fjords from the fjords prone to Atlantic water advection. The fjords with a limited water mass exchange incorporated local or Arctic-type waters and were host to specific zooplankton communities and particles, with the marked presence of species adapted to high particle concentrations (Microsetella norvegica) or species of Arctic affiliation (Calanus glacialis). In the open fjords, zooplankton communities were characterised by the predomination of Oithona similis and Calanus finmarchicus, confirming influence of Atlantic water. The zooplankton community size structure, expressed as abundance, was mainly shaped by changes in the contributions of small copepods, whereas the size structure expressed as biovolume reflected the differences in the co-occurring sibling species of Calanus spp. and/or differences in their dominating life stages. The results of this integrative across-system study constitute a necessary baseline for the future monitoring of changes in the zooplankton communities, which are likely to occur in response to climate change at high latitudes.