As a main source of heat for the Arctic Ocean, the Atlantic and Summer Pacific waters and their spatiotemporal variability require serious attention especially in the context of a drastic summer sea ice extent decrease. We propose to examine the recent evolution of these two water masses at a larger spatial scale than what was done so far. For that purpose, we introduced indices that proved to be efficient tools for quantifying water masses influence. Based on these indices and thanks to a very large data set collected throughout the Arctic deep basin from 1997 to 2008, we investigated the interannual variability of the Atlantic and Summer Pacific waters distribution and characteristics. Observations confirmed the existence of warm pulses of the Atlantic water mass propagating into the Arctic basin. However, no warming trend of the Atlantic water in the Eurasian basin was identified over the 1997–2008 time period. In contrast, the Summer Pacific water was getting warmer during the same period. The Summer Pacific water of the Canadian basin, being closer to the surface than the Atlantic water mass and exhibiting a warming trend, appears to be a serious candidate for contributing partly to the drastic summer sea ice extent and thickness decrease observed recently in the Arctic and in the Canadian basin in particular.