The Arctic has undergone significant changes in the last 20–30 years. The understanding of these changes is limited by the time span or resolution of existing climate records. The main gateway of heat to the Arctic Ocean is the Fram Strait, between Greenland and Svalbard. We have reconstructed past air and sea surface temperatures and relative variations in freshwater extent in a marine core from eastern Fram Strait which spans the last 2000 years. The results show a progressive increase in air temperature and a decrease in the upper mixed water layer temperature, together with an increase in freshwater content during the last 1000 years. Considering the oceanographic features of the eastern Fram Strait, these results suggest that there might have been a progressive increase in the inflow of Atlantic water during the last 1000 years, accompanied by an increase in atmospheric heat transport, causing progressive sea-ice melting and subsequent cooling and freshening of the upper mixed water layer in this area. We suggest that our data show long-scale average changes in the modes of positive and negative Arctic multidecadal variability over the last 2000 years.