Global challenges in removing heavy metal ions from aquatic reservoirs require novel solutions, especially the application of environmentally friendly materials. This paper presented the efficient removal of Fe3+ and Pb2+ ions from wastewater by apatite ore-based nanostructures. The synthesized material exhibited a nanostructure with high thermal stability, high porosity and negative surface potential, suitable for heavy metal removal in wastewater. The adsorption measurements performed in varying conditions (pH, mass of the adsorbent, and contact time onto the adsorbent) proved that even a few milligrams of the synthesized material could effectively absorb the lead and iron ions from the solution, reaching an effectiveness of about 90%. The maximum adsorption capacity followed the Langmuir isotherm model, estimated at 341 mg.g− 1 for Pb2+, and 1092 mg.g− 1 for Fe3+. Experiments conducted with industrial and craft-village’s wastewaters confirmed the high potential of the nanostructural chemically modified apatite as an efficient and affordable material for the removal of various pollutants from aqueous solutions in practical conditions.