Integrated Multi-Trophic Aquaculture (IMTA) has emerged as an environmentally sustainable aquaculture approach by integrating organisms from different trophic levels to improve nutrient recycling efficiency. This study evaluated the effectiveness of various IMTA species combinations in reducing Total Ammonia Nitrogen (TAN), Dissolved Inorganic Nitrogen (DIN), and Dissolved Inorganic Phosphate (DIP) within marine culture systems. A completely randomized design with four treatments and three replications was employed, comprising P1 (Lates calcarifer), P2 (Lates calcarifer + Perna viridis), P3 (Lates calcarifer + Caulerpa lentillifera), and P4 (Lates calcarifer + Perna viridis + Caulerpa lentillifera). Water samples were collected every 15 days over a 45-day culture period and analyzed using UV–Visible spectrophotometry. Nutrient reduction efficiency was calculated for each treatment, while one-way Analysis of Variance (ANOVA) followed by Tukey's post hoc test was applied to determine significant differences among treatments. The results demonstrated that integrated culture systems consistently reduced nutrient accumulation more effectively than monoculture. The complete IMTA treatment (P4) exhibited the greatest capacity to regulate TAN, DIN, and DIP concentrations through complementary nutrient uptake by macroalgae and filtration by bivalves. ANOVA confirmed significant treatment effects on TAN (F = 6.24, p = 0.021), DIN (F = 5.87, p = 0.016), and DIP (F = 5.21, p = 0.021). These findings demonstrate that integrating Lates calcarifer, Perna viridis, and Caulerpa lentillifera substantially enhances nutrient recycling efficiency, improves water quality, and provides an ecologically sustainable strategy for tropical marine aquaculture.