Cultured bivalves, Crassostrea gigas and Tapes philippinarum efficiently removed particulate matter from fish-pond effluents under two hydrological regimes. Two reactor types, a Plug Flow Reactor and a Continuous Stirred Flow Reactor were tested. Under the experimental conditions, the Plug Flow Reactor was found to be more efficient in deputing aquaculture effluents. A mixture of juvenile bivalves of both species further increased treatment efficiency. Flow rate and reactor length influence vertical settling of the non-planktonic particles. A mathematical model is proposed to predict particle removal by the bivalves under the conditions of the two rector types.