Aquaponics is the integration of recirculating aquaculture and hydroponic systems which is considered to be an innovative, eco-friendly and sustainable food production technology. In this study, a special design of hydroponic biofilter that integrated constructed wetlands and floating-raft rice hydroponics was constructed to treat the nutrient rich effluents from the intensive fishpond and to establish an aquaponic system on pond scale. The treatment efficiencies and food production potential of the new rice hydroponic biofilter was evaluated after determining the key operating parameters. As the results, overall nutrient removal efficiency was optimized at hydraulic load rate (HLR) of 0.58 m.d−1 and air-to-water ratio of 2:1. The average removal efficiencies of total ammonia nitrogen (TAN), total nitrogen (TN), total phosphorus (TP) and chemical oxygen demand (CODMn) from fishpond wastewater were in the range of 33.75–34.31%, 59.21–64.53%, 68.43–73.75% and 71.66–74.37%, respectively. Meanwhile, hydroponic rice grew well in the biofilter and gained a yield of 7 127 kg.ha−1. These results probably implied that the novel rice hydroponic biofilter exhibited efficient effluent treatment and presented as a viable alternative for the food production in a pond-scale aquaponics recirculating system.