Dissolved oxygen (DO) can be influenced by both physical and biogeochemical conditions of the ocean and is hence an important index for predicting changes in ocean environments. However, the relationship between biogeochemical activities and the DO concentration has not been quantified clearly in the Japan Sea (JS). In this study, we developed a coupled physical-biogeochemical model and clarified the contributions of biological processes to the DO content in the upper JS. We conducted two numerical experiments: with and without the biogeochemical compartments. Taking the biogeochemical factors into account gave better estimations for the spring-to-autumn seasonal migration of the subsurface DO maximum. In the euphotic zone, high photosynthetic production increases the DO concentration from spring to autumn. The strongest positive effect of biological processes on DO concentrations appears in summer at a depth of 30 m and is more than 0.5 ml l−1. As summer progresses to autumn, the vertical pattern of DO concentration in the Tsushima Warm Current (TWC) region shows minima at depths between 50 and 100 m, which is caused by the intrusion of low DO water from the East China Sea. The strongest negative effect on DO concentrations mainly due to the decomposition of detritus occurs in the TWC region below 150 m depth because the water is poorly ventilated by the relatively weak winter convection.