In a warmer Arctic with less sea ice and stronger stratification, the environmental changes are expected to impact the pelagic food web, but few biological studies supporting this exist compared with the well‐documented physical changes. Here, we analyze a subset of 13 yr of data from Disko Bay, Western Greenland, from the period 1992 to 2018 for trends in the key zooplankton genus Calanus during May and June in relation to physical conditions. In the 1990s, the small North Atlantic species Calanus finmarchicus and the two larger Arctic species Calanus hyperboreus and Calanus glacialis contributed equally to the copepod biomass. With the reduction in sea ice cover, however, the Arctic species have declined, and currently C. finmarchicus dominates the biomass. Because of the species shift, the Calanus community is now dominated by smaller individuals and the lipid content of Calanus females during spring and summer has decreased by 34%. Moreover, during the last decade the annual variation in population size has been prominent, Calanus virtually being absent in some years. Because of the central role of Calanus in the Arctic food web, the changes will likely impact higher trophic levels, including fish, sea birds, and marine mammals.