Over the years, aquaponics has become a powerful technological tool that allows the sustainable production of food, integrating conventional fish farming with vegetable production. The present study evaluated the production of late seedlings of açai Euterpe oleraceae in an aquaponic system with tambaqui Colossoma macropomum. A total of 36 tambaquis with an initial average weight and length of 1086.75 ± 16.38 g and 38.49 ± 0.90 cm were distributed in 12 independent aquaponic units, totaling 3.62 kg m−3. The fish were fed three times daily with commercial feed at a rate of 3%. Three flooding levels of 5, 10 and 15 cm, with constant water flow through the hydroponic bed (0.5 m2), were evaluated, and a control-hydroponic bed with flooding levels of 10 cm was established, all in triplicate. In the 5 and 10 cm treatments, 3450 açai seedlings with an initial height of 12.3 ± 1.9 cm were used (575 per aquaponic units), while the 15 cm treatment contained non-germinated açai seeds. The control group did not receive açai seeds and remained empty. Analyses to monitor total dissolved solids (TDS), electrical conductivity, dissolved oxygen, temperature, pH, alkalinity, hardness, nitrogenous compounds, and phosphate levels were performed. At the end of the 30-day trial, the growth performance of tambaqui and plants was evaluated. Water quality was significantly (p < 0.05) affected by different flooding levels. Electrical conductivity and TDS decreased with an increasing in flooding levels. The flooding levels significantly influenced (p < 0.05) the concentration of total ammonia and nitrate between the treatments. The 5 cm flooding level showed the best plant development indexes for total height, aerial portion height, root height and aerial portion fresh mass. No significant differences (p < 0.05) were observed in tambaqui growth performance. The aquaponic system proved to be effective in reusing fish waste (excreta and feed leftovers) generated in the system. The biotransformation of waste into nutrients allowed the growth of plants and nitrifying bacteria, which, through their metabolic pathways, ensured the purification and reuse of water, avoiding the discharge of this waste into the environment.