The metabolism and the fate of 14C labelled carbon was examined in 4 outdoor mesocosm (13 m3) tanks containing both benthic and pelagic compartments. Mesocosms with (16/m2) and without the clam, Mercenaria mercenaria were compared. System production, net and gross sedimentation of particulate carbon and benthic remineralization of dissolved inorganic nitrogen were all greater in mesocosms with clams. A filtration rate model, dependent on clam size and temperature, explained between 74–114% of the increased gross sedimentation in clam tanks relative to controls.The higher production in the clam tanks was at least in part due to a greater flux of dissolved inorganic nitrogen from the benthos. Despite this greater production in the clam tanks, water column biomass remained similar to controls. Calculations based on the filtration rate model indicated that clams could have consumed between 30% and 46% of the excess biomass produced during the day. Loss of particles due to processes in the water column appeared to consume most of this excess biomass. Although clams enhanced production and sedimentation, they did not limit phytoplankton biomass in the water column through filtration.