The water mass changes in the Makarov Basin and adjacent areas associated with the recent loss of Arctic sea ice had not been studied in detail. We combined data obtained from multiple cruises in these regions and used chemical tracers to investigate the spatial and temporal changes in water masses. Our data show that a previously present temperature maximum water has disappeared from the Makarov Basin and Chukchi Abyssal Plain due to enhanced cooling and convection in the East Siberian Sea. In addition, a large volume of water has formed by cooling and convection and is flowing into the Makarov Basin, producing a temperature minimum with relatively high nutrients and resulting in a shoaling of the nutricline. This temperature minimum water likely originated from the eastern part of the East Siberian Sea, where significant open water areas appeared after 2005 in the freeze-up season. The water mass boundary between this temperature minimum water and the Pacific-origin temperature minimum water shifted westward from the Chukchi Plateau in the early 2000s to the Mendeleyev Ridge in the late 2000s, probably owing to a westward flow of the enhanced Beaufort Gyre associated with recent sea ice loss in the Canada Basin. Although the shoaling of the nutricline in the Makarov Basin could increase phytoplankton production, such production could decrease in the southern Makarov Basin because a large amount of sea ice meltwater covers that region and might decrease the nutrient supply from the subsurface layer.