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Different fertilization regimes in biofloc systems influence the predominance of distinct bacterial populations, impacting water quality and organism performance. This study evaluates the growth and nutrient absorption of the macroalgae Ulva lactuca when cultivated in an integrated system with Penaeus vannamei and Oreochromis niloticus in chemoautotrophic and heterotrophic systems. The experiment lasted 45 days and comprised two treatments, each with three replicates: chemoautotrophic—utilizing chemical fertilizers; heterotrophic—employing inoculum from mature biofloc shrimp cultivation, supplemented with organic fertilizers. Each treatment consisted of three systems, each containing a 4 m3 tank for shrimp, 0.7 m3 for tilapia, and 0.35 m3 for macroalgae, with continuous water circulation between tanks and constant aeration. Water quality analyses were carried out during the experiment, as were the performances of the macroalgae and animals. The data were subjected to a statistical analysis. Results revealed an increase in macroalgae biomass and the removal of nitrate (57%) and phosphate (47%) during cultivation, with a higher specific growth rate observed in the chemoautotrophic treatment. Nonetheless, the heterotrophic treatment exhibited higher levels of protein in the macroalgae (18% dry matter) and phosphate removal rates (56%), along with superior maintenance of water quality parameters. Tilapia performance varied across treatments, with a higher final weight and weight gain recorded in the heterotrophic treatment. The recycling of water from an ongoing biofloc cultivation with organic fertilization demonstrated viability for macroalgae cultivation within an integrated system involving shrimp and fish.