Description: Zooplankton in Kongsfjorden, Svalbard, is shaped by irregular advection of seawater from the West Spitsbergen Current as well as input of freshwater of glacial and riverine origin. The zooplankton community reflects contributions of Arctic vs. Atlantic water masses in the fjord, and is changing with increasing temperature and declining sea ice. Here, we review zooplankton studies from Kongsfjorden, and present new data from a 20-year time series (1996–2016) of zooplankton abundance/biomass in the fjord based on annual surveys during summer. During the last decade, the marine environment of the West Spitsbergen Shelf and adjacent fjords has undergone changes with increasing temperatures and volume of inflowing Atlantic Water and declining sea ice. Annual monitoring of mesozooplankton since 1996 has shown high seasonal, spatial, and inter-annual variation in species abundance and biomass, and in the proportion of Atlantic and Arctic species. Inter-annual variations in species composition and abundance demonstrate fluctuating patterns related to changes in hydrography. “Warm years” in Kongsfjorden were characterized by higher abundances of Atlantic species, such as Calanus finmarchicus, Oithona atlantica, Thysanoessa longicaudata and Themisto abyssorum. Other krill species, particularly Thysanoessa inermis and to a lesser extent T. longicaudata, increased in abundance during the warming period in 2006–2007, mainly in the inner basin. “Cold years”, on the other hand, were characterized by higher abundance of Themisto libellula. There was no clear impact, however, of changes in environmental factors on the abundance or biomass of the Arctic species Calanus glacialis suggesting that the changes in environmental conditions have not reached critical levels for this species. The long-term zooplankton data demonstrate that some Atlantic species have become more abundant in the Kongsfjorden’s pelagic realm, suggesting that they may benefit from increasing temperature, and also that the total biomass of zooplankton has increased in the fjord implying potentially higher secondary production.