Nine recirculating aquaculture systems utilizing three biofilter types were placed on line and stocked with yellow perch, Percaflavescens, fingerlings. Biofilter type differed among systems, and included upflow pulsed bed bead filter, packed tower trickling filter, and rotating biological contactor. Following filter acclimation, a comparative analysis of biofilter performance was conducted, involving measurement of temperature, pH, dissolved oxygen, total ammonia-nitrogen, nitritenitrogen, nitrate-nitrogen, alkalinity, total hardness, carbonaceous biochemical oxygen demand, dissolved organic carbon, and total suspended solids. Filter bed emergence promoted effective carbon dioxide stripping, pH maintenance, and consistent nitrification performance in trickling filters and rotating biological contactors. Higher total ammonia nitrogen mass removal rates were observed in trickling and rotating biological contactor filters than in bead filters. Low total ammonia nitrogen mass removal rates and nitrification efficiencies for all filters resulted from relatively high carbonaceous biological oxygen demand loadings. Analysis of areas under mass removal curves showed that RBC filters were surface area limited. Foam formation in trickling filters effectively removed total suspended solids from the culture water. Filter type did not have a significant effect on median organic water quality parameter values in the production tanks. Although differences in nitrification performance and certain water quality parameters were observed between filter types, the data set did not indicate that one filter type should be considered generally most effective at treating wastewater produced in a recirculating aquaculture system.