Micro-pollutants, especially antibiotics contamination in water bodies, are a serious concern, and their detection at a low level is important for human health and even aquatic life at large. The present investigation aims to obtain the novel nanocomposite material precursor to clay and silane. The nanocomposite material is decorated with Ag or Au nanoparticles as obtained indigenously by a green route using natural phytochemicals. The materials were extensively characterized by advanced analytical methods. The nanocomposite materials (Ag(NP)/TCBN and Au(NP)/TCBN) are employed in the selective and efficient trace measurement of sulfamethoxazole (SMZ) in aqueous solutions using the differential pulse anodic stripping voltammetry. The cyclic voltammetric and electrochemical impedance spectroscopic methods showed an increased electroactive surface area as well as faster electron transfer reactions compared to the glassy carbon electrode (GCE). The DPASV measurements at the concentration range of 0.25 mg l−1 to 30.0 mg/l showed that the novel nanocomposites provide the LOD of 0.022 and 0.036 mg l−1, respectively, for the Ag(NP)/TCBN/GCE and Au(NP)/TCBN/GCE for sulfamethoxazole. Further, the application of the method for the detection of sulfamethoxazole in real water samples resulted in an acceptable recovery percentage of 93.08 to 103.7.