A model system is proposed, in which particulate and dissolved metabolites from the effluents of fish culture are removed by biofilters of bivalves (Crassostrea gigas and/or TaPes semidecussatus) and seaweeds (Ulva lactuca). The design utilizes ecological principles and the results of long-term pilot-scale trials with each of the four components of the system. Fresh sea water enters the fishponds, drains through an earthen sedimentation pond, a bivalve filtration unit and a seaweed filtration/production unit, and is finally discharged back into the sea. An additional loop recirculates water from the sedimentation pond through a bivalve production unit. The performance of each of the different components of the system is assessed in terms of total nitrogen budgets, which yield the following results: fish yield, 26% of the N introduced in the feed; bivalve yield, 14.5%; seaweed yield, 22.4%; settled feces, 32.8%; suspended and dissolved discharge back into the sea, only 4.25%. The harvested yields contain 63% of the N budget. The production of 1 kg of fish, requiring 3 kg of feed, is accompanied by the production of 3 kg of bivalves and 7.8 kg of seaweed. Each 100 m2 of fishponds requires 50 m2 of sedimentation ponds, 33 m3 of bivalve troughs and 42 m2 of seaweed ponds.