Hydroxyapatite (Ca10(PO4)6(OH)2) calcium phosphate is a robust and viable magnetic material for the treatment of polluted air, water, and soil. Because of its unique structure and appealing properties such as high adsorption capabilities, acid-base adaptability, ion-exchange capability, and thermal stability, hydroxyapatite (HAp) has a lot of potential in the field of environmental management. An aqueous extract of Monoon longifolium leaves was used for the preparation of hydroxyapatite nonparticles as the adsorbent for fluoride ion removal from aqueous solution in this work, resulting in bio-based hydroxyapatite nanoparticles. The prepared adsorbent was characterized by using instrumental techniques such as TGA/DTA, XRD, AAS, FT-IR, and UV-Vis spectroscopy as well as SEM. The batch adsorption approach was used to determine the optimum adsorption efficiency of HAp NPs under various experimental conditions. As a result, the best removal efficiency corresponds to 0.75 g HAp NPs, 15 mg/L, and pH 7 at 50 minutes (96%). The equilibrium adsorption data were better fitted into the Freundlich isotherms (R2 = 0.99), and the pseudo-second-order kinetic model was found to be suitable (R2 = 0.99) for the kinetic model. Fluoride ion adsorption on HAp NPs is spontaneous, endothermic, and possible at temperatures over 318 K, according to thermodynamic calculations. The results hint at a conclusion that the synthesized HAp NPs were an efficient adsorbent for the removal of fluoride ions and the overall process can be an economical choice for scaled-up water treatment processes.