The effects of hydrothermal treatment, 0–5% KMnO4 content, and 300–400 °C pyrolysis temperature, were studied for activated carbon preparation from sugar cane leaves in comparison with non-hydrothermal treatment. The percent yield of activated carbon prepared by the hydrothermal method (20.33–36.23%) was higher than that prepared by the non-hydrothermal method (16.40–36.50%) and was higher with conditions employing the same content of KMnO4 (22.08–42.14%). The hydrothermal and pyrolysis temperatures have the effect of increasing the carbon content and aromatic nature of the synthesized activated carbons. In addition, KMnO4 utilization increased the O/C ratio and the content of C-O, Mn-OH, O-Mn-O, and Mn-O surface functional groups. KMnO4 also decreases zeta potential values throughout the pH range of 3 to 11 and the surface area and porosity of the pre-hydrothermal activated carbons. The use of the pre-hydrothermal activated carbon prepared with 3% KMnO4 and pyrolyzed at 350 °C as a filter in an aquaponic system could improve the quality of water with pH of 7.2–7.4, DO of 9.6–13.3 mg/L, and the turbidity of 2.35–2.90 NTU. It could also reduce the content of ammonia, nitrite, and phosphate with relative removal rates of 86.84%, 73.17%, and 53.33%, respectively. These results promoted a good growth of catfish and red oak lettuce.