Sessile filter-feeding marine sponges (Porifera) have been reported to possess high efficiency in removing bacteria pollution from natural or aquaculture seawater. However, no investigation has been carried out thus far in a true mariculture farm water system. Therefore this study sought to investigate the ability of the marine sponge Hymeniacidon perlevis to bioremediate the bacteria pollution in the intensive aquaculture water system of turbot Scophthalmus maximus. Sponge specimens were hung in fish culture effluent at different temperature to investigate the optimal temperature condition for bacteria removal by H. perlevis. Turbots S. maximus were co-cultured with sponge H. perlevis in 1.5 m3 of water system at 15–18°C for 6 weeks to control the growth of bacteria. It was found that H. perlevis was able to remove pathogenic bacteria efficiently at 10–20°C, with a maximal removal of 71.4–78.8% of fecal coliform, 73.9–98.7% of pathogenic vibrio, and 75.0–83.7% of total culturable bacteria from fish-culture effluent at 15°C; H. perlevis continuously showed good bioremediation of bacteria pollution in the S. maximus culture water system, achieving removal of 60.0–90.2% of fecal coliform, 37.6–81.6% of pathogenic vibrio, and 45.1–83.9% of total culturable bacteria. The results demonstrate that H. perlevis is an effective bioremediator of bacteria pollution in the turbot S. maximus culture farm water system. Biotechnol. Bioeng. 2010;105: 59–68. © 2009 Wiley Periodicals, Inc.