The green mussel Perna viridis (green mussel) is a promising bioremediator for the Penaeus monodon (giant tiger shrimp) Integrated Multitrophic Aquaculture (IMTA) pond systems in Northern Mindanao, Philippines. This study contributes to refine an IMTA pond technology by assessing the efficiency of P. viridis in removing total heterotrophic bacteria (THB), Vibrio, and plankton at different stocking densities (0-control, 10, and 15 mussels−200 L) from P. monodon pond culture medium (water and soil). Experiments were conducted under microcosm conditions using plastic drums, with bioremediation monitored over 72 h and filtration rates assessed over 24 h. THB and Vibrio counts (LOG CFU·mL⁻1) in the water were significantly higher in control (1.47E + 02 to 1.55E + 03 THB; 5.33E + 01 to 7.70E + 02 Vibrio) than in 10 mussels−200 L (1.40E + 02 to 5.58E + 02 THB; 5.50E + 01 to 1.98E + 02 Vibrio) and 15 mussels−200 L (1.54E + 02 to 5.67E + 02 THB; 5.42E + 01 to 1.93E + 02 Vibrio). Plankton densities (cells·mL⁻1) in the control (5.8E + 03 to 6.3E + 03) significantly increased towards the culture period, while the remaining treatments declined but no significant difference with each other (10 mussels−200 L: 5.8E + 03 to 2.2E + 03; 15 mussels−200 L: 5.9E + 03 to 1.9E + 03). Filtration rates after 24 h were 239 mL h⁻1 mussel⁻1 at 15 mussels−200 L and 229 mL h⁻1 mussel⁻1 at 10 mussels−200 L. Elevated temperature and slightly reduced dissolved oxygen were observed during the culture, possibly affecting the filtration rates of the mussels. Chlorophyll a levels were also significantly lower in mussel treatments compared to the control. The results indicate that P. viridis, regardless of the stocking density, effectively reduced THB and Vibrio (72 h) and plankton densities (24 h) using IMTA pond culture medium. However, the 10 mussels−200 L stocking density is recommended for bioremediation to minimize competition and waste accumulation in the IMTA pond system.