Akkeshi Lake is a typical subarctic estuary located in Hokkaido, Japan; it is covered with eelgrass, specifically Zostera marina. The oyster Crassostrea gigas is cultured throughout the lake, except for on the intertidal sand flats, where the Manila clam, Ruditapes philippinarum, is cultured near the mouth of the lake. To estimate the particulate organic carbon (POC) flux of various sources, including eelgrass, flowing out from Akkeshi Lake to Akkeshi Bay and to evaluate the role of eelgrass in carbon transport, we developed an ecosystem model that includes phytoplankton, zooplankton, dissolved inorganic matter (DIM), dissolved organic matter (DOM), particulate organic matter (POM), eelgrass, epiphytic algae, oysters and the Manila clam, and separated POM into eight classes according to its sources. Eelgrass and epiphytic algae are the most important sources of POC in Akkeshi Lake, especially in the litterfall season. The total POC inflow/outflow quantities to/from Akkeshi Lake during nine months from April to December was -4648 tons; according to its sources, -4414 tons (outflow) came from eelgrass and epiphytic algae, -551 tons (outflow) from oysters and the Manila clam, 145 tons (inflow) from phytoplankton and zooplankton, 383 tons (inflow) from outside sources (i.e., open sea) and -211 tons (outflow) from the river. The total POC production was approximately 75727 tons, 89% of which was from eelgrass and epiphytic algae; 7% was from oysters and the Manila clam; 3% was from phytoplankton and zooplankton; and 1% was from river.