This study investigated the potential of the marine sponge Hymeniacidon perlevis (H. perlevis) for bioremediation of bacterial pollution in the water systems used for turbot (Scophthalmus maximus) mariculture. Sponge specimens were introduced into fish culture effluent, and their bacterial removal efficiency was assessed at various temperatures. The optimal bacterial removal conditions were found to be within a temperature range of 15–18 °C. Over 6 weeks in a 1.5 m3 pilot-scale aquaculture system, the sponge demonstrated significant bacterial removal capabilities. It effectively eliminated several bacterial types, including faecal coliforms, pathogenic Vibrio, and total culturable bacteria. The highest removal rates were observed at 15 °C, with the sponge removing 71.4–78.8% of faecal coliforms, 73.9–98.7% of pathogenic Vibrio, and 75.0–83.7% of total culturable bacteria. Even at higher temperatures, H. perlevis maintained a steady performance, with bacterial removal rates ranging from 60.0% to 90.2% for faecal coliforms, 37.6% to 81.6% for pathogenic Vibrio, and 45.1% to 83.9% for total culturable bacteria. The sponge demonstrated a reliable and consistent capacity to mitigate bacterial contamination in the aquaculture system, indicating its potential as an effective bioremediation tool in marine mariculture settings.