Marine aquaculture is undeniably a key future direction for the production of food. However, traditional aquaculture involves some significant drawbacks, the major one of which is the surplus discharge of organic matter and dissolved nutrients. To mitigate the environmental impact, integrated multi‐trophic aquaculture (IMTA) systems, which advocate the integration of fed fish with inorganic and organic extractive species, may offer a sustainable solution. This study focuses on an innovative experimental setting, integrating three marine macroalgae species (Ulva rigida, Gracilaria conferta, Hypnea musciformis) serially connected via two‐stage seaweed culture tanks to a finfish culture (the gilthead sea bream; Sparus aurata). The aim was to compare and assess the biofiltration and growth performances of the seaweeds, while altering their order in the two‐stage system. The results indicated U. rigida as the fastest growing species. Ulva rigida also displayed the highest total ammonia nitrogen (TAN) uptake rates and removal efficiency. The design allowed the production of high tissue protein and carbohydrate levels for potential biorefinery uses. Ulva rigida protein content averaged 23%, while that of H. musciformis and G. conferta averaged 25% and 18%, respectively. Hypnea musciformis and G. conferta grown under low nutrient conditions presented a significantly higher total carbohydrate content of nearly 50%, compared to 34% exhibited by U. rigida. In summary, the seaweed pairing in a two‐stage system did not inhibit the performance of each individual species and improved overall production. Consequently, it offers significant advantages for future IMTA systems.