Semi-enclosed coastal seas act as transitional zones between terrestrial areas and open ocean. The active biogeochemical processes there play a crucial role in global material cycles. Nutrients from diverse sources collectively shape the nitrogen inventory and budget in the coastal oceans through the combined influence of physical dynamics and biogeochemical processes. In this study, we assess the relative contributions of different nutrient sources to the ecosystem of the Seto Inland Sea, a semi-enclosed sea in Japan. Using a three-dimensional coupled hydrodynamic–biogeochemical model with an embedded tracking technique, we show that the open ocean accounts for 61 % and 46 % to the inventories of dissolved inorganic nitrogen (DIN) and phytoplankton, respectively. The conversion of DIN into particulate organic nitrogen (PON) was also mainly driven by nitrogen from the open ocean, except during the summer. Riverine nitrogen primarily supported the deposition of PON to the seafloor, whereas the nitrogen from the open ocean dominated the PON flux exported to the open ocean. These results establish a baseline framework for the future assessments of coastal responses to global changes.