A nitrogen-based four-compartment ecosystem model coupled with a physical model is applied to the Japan Sea. Seasonal variability in ecosystem dynamics simulated by the coupled model is in good agreement with the observations. A set of artificial tracers labeled according to specified regions is introduced to identify nutrient sources in the surface layer of the Japan Sea. The results of the labeled tracer experiment show that one of the large nutrient sources in the southern Japan Sea is located along the east coast of Korea. The upward flux of dissolved inorganic nitrogen along the east coast of Korea and the nitrogen flux through the western channel of the Tsushima/Korea Straits (TKS) sustain high primary productivity in the southwestern Japan Sea. The surface nutrient conditions in the nearshore region along the Japanese coast depend on the nitrogen flux through the eastern channel of the TKS throughout the year. Since materials transported through the TKS have significant impact on the biological productivity of the southern Japan Sea, field observations of chemical and biological data, in addition to physical ones, should be continued in the TKS.