Aquaponic system, which integrates recirculating aquaculture system (RAS) and hydroponics together, maintains high stocking density of fish. In order to eliminate the risk of fish disease, antibiotics has been inevitably used due to human and environmental concern. This paper aims to analyse the potential risk of antibiotics pollution in aquaponic system and propose the control approaches. The removal of residual antibiotics from aqueous phase of aquaponics can be more efficient than the open system. An aquaponic system with comprehensive antibiotics pollution control strategy is proposed by combining the operational units of UV-photolysis and biofilter adsorption/biodegradation, which is expected to work efficiently and cost-effectively. The biofilter is developed by containing immobilized biofilm incorporated with activated carbon. The antibiotics in aquaponics are first decomposed in UV-photolysis unit for 6 h, the residual intermediate products of antibiotics are then adsorbed onto the activated carbon and biodegraded by the microbes in the immobilized media of the biofilter within 12 h. It concludes that aquaponic system with the integrated approaches is promising in effective utilization of antibiotics and removal of the residual antibiotics comparing with the conventional open aquaculture system such as pond, lake or reservoir.