Anthropogenic inputs of nutrients and trace elements have globally significant impacts on coastal waters. In order to evaluate the effect of the filter-feeding bay scallop Argopecten irradians on benthic−pelagic coupling in a eutrophic estuary (Laizhou Bay), biodeposition of total suspended materials, particulate nutrient (C, N, P) and trace elements (Cu, Zn, Pb, Cr, Cd, Hg, As) were determined using modified sediment traps during autumn 2013. Results showed that biodeposition rates of the bay scallops were rather high compared with those reported for other bivalves. The allometric relationship between the biodeposition rate (BDR; g ind. −1 d −1) and soft tissue dry weight (W; g ind. −1) was modeled (BDR = aW b) with the value of a being 1.24 in September and dropping to 0.96 in October. The biodeposition contributed to the enrichment of organic matter, C and N in the local sediment. Trace element concentrations in the scallop biodeposits were significantly higher than those of the natural surrounding sediments, especially during the months of October and November. A. irradians significantly increases the mass fluxes from the water column to the bottom, with estimated 1140 tonnes of total suspended material being deposited to the seabed each day in the culture zone. Results also suggest that biotransformation and biodeposition by such efficient filter-feeders may play a pivotal role in the fate and transportation of particulate nutrient and trace elements in aquatic ecosystems. In coastal waters and estuaries subject to anthropogenic inputs, suspended bivalve aquaculture could be environmentally advantageous via intense filtering and biodeposition, potentially mitigating eutrophication and trace element pressures.