Water from shrimp aquaculture ponds was circulated through a mangrove woodlot, oyster beds, and seaweed ponds in biofilter experiments designed to reduce environmental loads. Though the nutrient concentrations in the shrimp culture ponds were lower than those in the other ponds in many cases, the Chl. α concentration increased explosively in shrimp ponds and exceeded 160 μg/L. These results suggested that nutrients were used for the growth of phytoplankton. The Chl. α concentration was very low in the oyster pond, and it was suggested that oyster feed actively on phytoplankton. Ammonia was always lower in the seaweed ponds than in the oyster ponds, which suggested that seaweed took up ammonia. From the nitrogen budget, 27% of nitrogen in supplied feed was incorporated into shrimp, 32% was flowed to mangrove, oyster and seaweed ponds and removed with these biofilters, and 9% was added in the aquaculture system as dissolved inorganic and particulate nitrogen. Therefore, this aquaculture system using mangroves, oyster and seaweed as biofilters was thought to be effective to reduce the environmental load.