[1] The magnitude of geothermal heating in the East/Japan Sea is about 100 mW/m 2 , twice that of a typical abyssal plain. In addition, bottom stratification in the East/Japan Sea is much weaker than that typical of the open ocean. Thus, geothermal heating could have more prominent effects in the East/Japan Sea than in the open ocean, and we tested this hypothesis via numerical modeling. With less than 100 mW/m 2 bottom heat flux, we were able to reproduce bottom mixed layers that are thicker than~1000 m as observed. Previously, no numerical model has been successful in reproducing such bottom mixed layers. Geothermal heating intensifies the bottom flows but the simulated flows are not as strong as the observed ones. Over the northern part of the East/Japan Sea, reduction in deep stratification strengthens deep water mass formation, intensifying cyclonic circulations located over this area, so the effects of the heating extend to the surface. As the cyclonic circulation becomes stronger, the water at the center of the gyre is trapped and more exposed to cold air, so it becomes cooler, and colder deep water is produced. When the geothermal heating is strong enough, the surface cooling effect dominates the bottom heating and the deep layer becomes cooler showing that the nonlinear effects of geothermal heating are far reaching. Thus, to account for the observed dynamics, the full three-dimensional circulation at the basin scale is needed.