The bottom sowing of Manila clam and the interaction of Manila clam and eelgrass seedlings are affected by the exchange fluxes of nutrients at the sediment-water interface. It is considered that body size, abundance, and activity of Manila clam influence the exchange fluxes. To verify the hypothesis, Manila clams with different body sizes, abundances, and activities were cultivated by sediments for 19 d, during which the exchange fluxes were studied. The biomass, body size, abundance, and activity of Manila clam affected the exchange fluxes of nutrients. On the 13th day, the fluxes of NO2--N、NH3-N、TN were affected by body size, and the exchange fluxes of NO2--N and NH3-N increased as body size increased. On the 13th and 19th day, the exchange fluxes of NO2--N, NH3-N, TN, PO43--P were affected by the abundance and increased as abundance increased. Thus, the roles of biomass, body size, and abundance of shellfish should be considered to determine the carrying capacity for filter-feeding shellfish and clarify the interaction between shellfish and seagrass.