Intensive pond cultivation of Gracilaria may achieve maximal yields by enrichment of seawater with ammonia and CO2. In the present study, we examined the use of organic waste material as a source of ammonia and inorganic carbon. A biofiltration system was constructed, consisting of several fermentation tanks and a fluidized bed reactor for the required bioconversion of organic wastes. Gracilaria conferta was cultured in a 30m2 pond from which seawater was circulated through the biofiltration system for a period of nine months. As compared to the filtered seawater used for water supply, the outlets of the fermentation tanks and the fluidized bed reactor showed significant increases in dissolved inorganic carbon and ammonia concentrations and significant decreases in oxygen concentrations and redox potentials. The most efficient organic waste compound tested had the highest C/N ratio. No significant differences were found between the Gracilaria yields of the control and biofiltration pond systems. These results might contribute a fundamental improvement in the economy of Gracilaria pond cultivation by water recycling through such a biofiltration system. Statement of relevance The system might contribute a fundamental improvement in the economy of Gracilaria pond cultivation.