AbstractClimate change is especially strong in the region of the Arctic Ocean, and will have an important impact on its thermo‐haline structure. We analyze the results of a hindcast simulation of a new 3D ocean model of the Arctic and North Atlantic oceans for the period 1970–2019. We compared the time period 1970–1999 with the time period 2010–2019. The comparison showed that there is a decrease of stratification between the two periods over most of the shallow Arctic shelf seas and in the core of the Transpolar Ice Drift. Fresh water inputs to the ocean surface decline, and inputs of momentum to the ocean increase, which can explain the decrease in stratification. The comparison also showed that the mixed layer becomes deeper during winter, in response to the weakened stratification owing to increased vertical mixing. The comparison of summer mixed layer depths between the two time periods follows a deepening pattern that is less evident. Regional exceptions include the Nansen Basin and the part of the Canadian Basin bordering the Canadian Archipelago, where the mixed layer shoals. Trends of freshwater fluxes imply that the changes of haline stratification in these regions are also influenced by other processes, for example, horizontal advection of fresh water, increased mixing and changes in the underlaying water masses. Runoff increase toward the Arctic Ocean can locally decrease but also increase salinity, and has an impact on stratification which can be explained by coastal dynamics. The results emphasize the non‐linear nature of Arctic Ocean dynamics.