Bivalve has an important role in the marine ecosystem of Akkeshi estuary, which is located in eastern Hokkaido, Japan. To discuss the role of benthos and epiphyte on the material cycle in this area, we modified a three-dimensional physical-biological coupled model (MK-3). The ecosystem model includes eelgrasses, epiphytes, oysters and clams together with phytoplankton, zooplankton, POM and DOM and is based on nitrogen and phosphorus cycles. A physical model was forced by M2 tide. In this area, the role of clams on the material cycle is much larger than that of oysters, and epiphytes uptake nutrient twice as large as phytoplankton. We estimated nutrient release from sediment was smaller than previous estimation in sensitivity analysis, and we found that eelgrasses and epiphytes had an important role in supply for the food of clams and oysters.