Euphausiid (krill) and amphipod dynamics were studied during 2006–2011 by use of plankton nets in Kongsfjorden (79�N) and adjacent waters, also including limited sampling in Isfjorden (78�N) and Rijpfjorden (80�N). The objectives of the study were to assess how variations in physical characteristics across fjord systems affect the distribution and abundance of euphausiids and amphipods and the potential for these macrozooplankton species to reproduce in these waters. The abundances of euphausiids and amphipods were higher in Kongsfjorden than in Rijpfjorden and Isfjorden, and the highest abundances were observed at the innermost stations of Kongsfjorden, where Thysanoessa inermis and Themisto libellula dominated. The Atlantic species Thysanoessa longicaudata, Meganyctiphanes norvegica and Themisto abyssorum dominated at the outside Kongsfjorden. Inter-annual and seasonal variability in abundances of euphausiids and amphipods were evident. The presence of ripe euphausiids outside Kongsfjorden indicates that they may reproduce in these areas. Mature individuals of T. abyssorum were recorded mainly outside Kongsfjorden, whereas no mature or ripe T. libellula were present in both the inner and outer parts of this fjord. If the warming trend persists, as seen during the last decade, this would favour the Atlantic/boreal euphausiid species, while Arctic species, such as the amphipod T. libellula, may decline. Euphausiids and amphipods are major food of capelin (Mallotus villosus) and polar cod (Boreogadus saida), respectively, in this region, and changes in prey abundance will likely have an impact on the feeding dynamics of these important fish species.