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.

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Marine macroalgae are considered an untapped source of healthy natural metabolites and their market demand is rapidly increasing. Intertidal macroalgae present chemical defense mechanisms that enable them to thrive under changing environmental conditions. These intracellular chemicals include compounds that can be used for human benefit. The aim of this study was to test cultivation protocols that direct seaweed metabolic responses to enhance the production of target antioxidant and photoprotective biomaterials. We present an original integrated multi-trophic aquaculture (IMTA) design, based on a two-phase cultivation plan, in which three seaweed species were initially fed by fish effluents, and subsequently exposed to various abiotic stresses, namely, high irradiance, nutrient starvation, and high salinity. The combined effect of the IMTA’s high nutrient concentrations and/or followed by the abiotic stressors enhanced the seaweeds’ content of mycosporine-like amino acids (MAAs) by 2.3-fold, phenolic compounds by 1.4-fold, and their antioxidant capacity by 1.8-fold. The Sun Protection Factor (SPF) rose by 2.7-fold, and the chlorophyll and phycobiliprotein synthesis was stimulated dramatically by an order of magnitude. Our integrated cultivation system design offers a sustainable approach, with the potential to be adopted by emerging industries for food and health applications.