Malachite Green (MG) is commonly used in aquaculture as a therapeutic agent on a global scale. However, its use in animals meant for food production is banned due to its potential carcinogenic effects and the prolonged presence of residues. Cloud point extraction (CPE) with UV-Vis spectropotometry were utilized to measure MG in 30 cold-water samples of farmed fish from Mazandaran province, Iran. The concentrations ranged between 0.014±0.002–0.506±0.02 mg/l. To remove MG, a hybrid magnetic nanocomposite of Fe3O4/CNT@polydopamine/hydroxyapatite (Fe3O4/CNT@PDA/HAP) was synthesized through a simple method and characterized successfully using VSM, BET, TEM, XRD, and FTIR spectroscopy. Batch experiments were conducted to study the impact of different parameters such as contact time, solution pH, and adsorbent dosage on the adsorption efficiency of Fe3O4/CNT@PDA/HAP. The highest MG adsorption efficiency (R= 84.5%) was achieved at pH =7.2, with 10 mg of adsorbent, and contact time of 30 min at room temperature. Fe3O4/CNT@PDA/HAP was also applied under optimal conditions to eliminate trace amounts of MG from cold-water samples in fish farming. The results demonstrate that the synthesized hybrid magnetic nanocomposite has the potential to remove MG from real water samples at very low concentrations.