Integrated multitrophic aquaculture (IMTA) is an innovative approach for sustainable aquaculture development and ecosystem services. The present study aimed to compare the growth performance, production, and quality of the culture environment in integrated systems with different species combinations in tanks, in parallel with the natural dynamics of aquaculture. The experiment was designed to assess the feasibility of using seabass (Dicentrarchus labrax) as the fed component of the IMTA system, in combination with two clam species—the carpet-shell clam (Ruditapes decussatus) and short-necked clam (Paphia undulata)—and the whiteleg shrimp (Litopenaeus vannamei) as extractive species. The control experiments (T0 and G0) involved monocultures of seabass (D. labrax), while other treatments were IMTA systems. Over a 60-day culture period, the results showed a significant decrease in ammonia levels in the clam-seabass integrated groups, whereas increasing shrimp density significantly raised ammonia levels in shrimp-seabass integrated ponds. Additionally, fish reared with 0.5kg/ 0.5m³ of P. undulata and 0.5kg/ 0.5m³ of R. decussatus exhibited better growth performance, protein efficiency ratio (PER), proximate composition (PPV), protein ratio, and ash content. Fish reared with 20 shrimp (L. vannamei) exhibited the highest values for protein ratio, ether extract, ash, and fiber content. Clams reared in treatment T5 showed better growth performance, while shrimp reared in G1 exhibited superior growth. The findings of this study suggest that IMTA systems outperform monoculture systems, highlighting the potential of IMTA for sustainable aquaculture by improving growth performance and reducing environmental impact.