Changes in the hydrography of the Arctic Ocean have recently been reported. The upper ocean has been freshening and pulses of warm Atlantic Water have been observed to spread into the Arctic Ocean. Although these changes have been intensively studied, salinity and temperature variations have less frequently been considered together. Here hydrographic observations, obtained by icebreaker expeditions conducted between 1991 and 2011, are analyzed and discussed. Five different water masses in the upper 1000 m of the water column are examined in five sub-basins of the Arctic Ocean. This allows for studying the variations of the distributions of the freshwater and heat contents in the Arctic Ocean not only in time but also laterally and vertically. In addition, the seasonal ice melt contribution is separated from the permanent, winter, freshwater content of the Polar Mixed Layer. Because the positions of the icebreaker stations vary between the years, the icebreaker observations are at each specific point in space and time compared with the Polar Science Center Hydrographic Climatology to separate the effects of space and time variability on the observations. The hydrographic melt water estimate is discussed and compared with the potential ice melt induced by atmospheric heat input estimated from the ERA–Interim and NCEP/NCAR reanalyses. After a period of increased salinity in the upper ocean during the 1990s, both the Polar Mixed Layer and the upper halocline have been freshening. The increase in freshwater content in the Polar Mixed Layer is primarily driven by a decrease in salinity, not by changes in Polar Mixed Layer depth, whereas the freshwater is accumulating in the upper halocline mainly through the increasing thickness of the halocline. This is especially evident in the Northern Canada Basin, where the most substantial freshening is observed. The warming, and to some extent also the increase in salinity, of the Atlantic Water during the early 1990s extended from the Nansen Basin into the Amundsen and Makarov basins, while the warm and saline inflows occurring during the 2000s appear to be confined to the Nansen Basin, suggesting that the warm and saline inflow through Fram Strait largely recirculates in the Nansen Basin.