Arctic amplification is known to accelerate the hydrological cycle in high-latitude landmass, which eventually leads to increased river discharge into the Arctic Ocean. However, the majority of climate models in Coupled Model Intercomparison Project 5 (CMIP5) tend to underestimate Arctic river discharge. This study elucidates the role of additional Arctic river discharge for the phytoplankton responses in the present and future climate simulations. In the present climate simulation, the additional freshwater input showed a decrease in the phytoplankton in spring due to the increasing sea ice, and in summer, it showed an increase in phytoplankton due to the surplus nitrate leftover from spring and induced vertical mixing. Similar processes occurred in future climate simulations. However, in those simulations, the major response region of phytoplankton to additional freshwater input was altered from the Eurasian Basin to the Canadian Basin and the East-Siberian Sea. This is because the current marginal ice zone in the Barents-Kara Sea, where phytoplankton mainly responds, moves toward the East-Siberian-Chukchi Sea. We suggest that Arctic river discharge is potentially an important contributing factor for Arctic ecosystems in both present and future climate that controls sea ice and nutrient distribution.