Zooplankton abundance and community structures were studied in three west Spitsbergen fjords at the beginning of the warm phase, which seem to have entered in 2006. Sampling was conducted in summer 2007 at stations distributed along transects in Hornsund, Isfjorden and Kongsfjorden. Variations in zooplankton standing stocks and community structures (assessing taxonomic diversity and zoogeographical affiliations) were analysed in relation to the environmental variables using multivariate techniques. The hydrographic conditions in Hornsund were influenced by the cold Arctic Water, whereas those in Isfjorden and especially in Kongsfjorden were, to a greater extent, under the influence of the warm Atlantic Water. High abundances of both meroplankton and holoplankton organisms were observed in Kongsfjorden, with high contributions of boreal and ubiquitous species (Calanus finmarchicus and Oithona similis, respectively). In Hornsund at the same time, the zooplankton consisted mainly of boreo-Arctic and Arctic species, the abundances of which were comparable along the West Spitsbergen Shelf. Our results indicate that the difference in hydrography had measurable effects on the zooplankton community in the study area. Furthermore, by comparing regions of contrasting oceanographic conditions, we present evidence as to how the zooplankton structure will change in the Arctic ecosystems if the warming trends continue to operate with the same dynamics. The advection of Atlantic waters to the Arctic seas may lead to changes in zooplankton structure, with increased abundance and contributions of boreal and small ubiquitous species. The 'warmer Arctic fjords' scenarios may also induce more rapid development of both holoplankton and meroplankton populations and, consequently, modify the trophic interactions in plankton communities.