The present invention relates to a two-stage biofilter reactor system for removing nitrogenous compounds from a recirculating aquaculture system. The system includes a aerobic nitrification unit and a downstream anaerobic denitrification unit, wherein both units have a mobile bed of suspended media whereon bacteria can grow and reduce nitrate and/or ammonia levels in the recirculating aquaculture system. Use of the two-stage system has the advantage of reducing the water exchange rates and consumption of salt when maintaining a saline effluent.