Nitrogen removal and changes to microbial communities in model flood/drain and submerged biofilters treating aquaculture wastewater

► Flood/drain biofilters were compared to submerged biofilters for the treatment of marine aquaculture wastewater. ► Analysis of 16s rRNA and amoA genes by T-RFLP revealed distinct bacterial communities in the submerged and flood/drain biofilters. ► Removal of organic nitrogen and ammonia was higher in flood/drain biofilters. Removal of nitrites and nitrates was better in submerged biofilters. ► The use of combined flood/drain and submerged biofilters may offer the best solution to the treatment of aquaculture waste.