Fluoride contamination in water has emerged as a pressing global issue. In this study, we have proposed a novel and promising approach for efficient deep soil water fluoride removal using a zinc oxide nanoparticle (ZnO NP)-activated carbon composite. The composite material is designed to enhance the adsorption capacity and efficiency in removing fluoride ions from deep soil water. The green synthesis method was used for preparing ZnO NPs from Strychnos potatorum seed powder, and these nanoparticles were coated on an activated carbon filter for water purification. The performance of the composite material, in this extensive column adsorption method, from the fluoride-contaminated water samples was evaluated. Parameters such as physiochemical parameters, initial fluoride concentration, contact time, and composite dosage are systemically investigated. The results demonstrate that the ZnO NP-activated carbon composite exhibits superior fluoride removal efficiency compared to pristine-activated carbon. The composite material achieves a remarkable fluoride removal capacity of 10 mg/g. In-depth characterization techniques such as UV–Vis spectroscopy were used to measure the strength of ZnO NP synthesis, and scanning electron microscopy (SEM) and X-ray diffraction (XRD) were employed to analyze the morphology and crystalline structure of the composite material. In conclusion, the potential of ZnO NPs/AC could instantly and easily remove toxic chemicals and make water potable.