The East Sea (Japan Sea), a small marginal sea in the northwestern Pacific, is ventilated deeply down to the bottom and sensitive to changing surface conditions. Addressing the response of this marginal sea to the hydrological cycle and atmospheric forcing would be helpful for better understanding present and future environmental changes in oceans at the global and regional scales. Here, we present an analysis of observations revealing a slowdown of the long-term deepening in water boundaries associated with changes of water formation rate. Our results indicate that bottom (central) water formation has been enhanced (reduced) with more (less) oxygen supply to the bottom (central) layer since the 2000s. This paper presents a new projection that allows a three-layered deep structure, which retains bottom water, at least until 2040, contrasting previous results. This projection considers recent increase of slope convections mainly due to the salt supply via air-sea freshwater exchange and sea ice formation and decrease of open-ocean convections evidenced by reduced mixed layer depth in the northern East Sea, resulting in more bottom water and less central water formations. Such vigorous changes in water formation and ventilation provide certain implications on future climate changes.