Indomethacin (IDM) is commonly prescribed for headaches, fever, and articular disease as a nonselective nonsteroidal anti-inflammatory drug (NSAID), inhibiting prostaglandin synthesis to reduce fever, inflammation, and pain. However, its extensive use has resulted in water reservoir contamination from human and veterinary waste. Recognizing the urgent need for sustainable water contamination prevention and human health concerns, researchers have focused on indomethacin detection. In response, an innovative interdisciplinary platform, merging nanoscience and electrochemical engineering, was created. Detailed examination of the structural, crystallographic features and morphological insights of the electrode modifier was conducted. The nanocomposite's hierarchical arrangement, utilizing hybrid heterojunction and quantum confinement, enables synchronized indomethacin detection with a low limit of detection (LOD) of 39.3 nM. The resulting sensor demonstrates a wide linear range (0.001−264.02 μM), along with high sensitivity, selectivity, and stability. Expanding its utility, the sensor was successfully applied to water and human urine samples, showcasing its effectiveness in monitoring the proposed platform's consistency. This advancement shows promise in enhancing the sustainable detection of indomethacin in both environmental and biological settings.