This study deals with the use of calcium hydroxyapatite (HAP) materials as adsorbents for removing heavy metal ions from polluted waters. The synthesis conditions (i.e. P/Ca stoichiometry and nature of the solvent) of HAP samples were properly varied in order to prepare three different samples with tuned properties. Stoichiometric hydroxyapatite, with Ca/P = 1.67 (s-HAP), Ca-deficient hydroxyapatite, with Ca/P < 1.67 (d-HAP), and hydroxyapatite precipitated from hydro-alcoholic solution (a-HAP) were prepared and used as adsorbents for copper and lead ions. Tests were carried out with simulated polluted waters containing single- and binary-metal concentrations of the two ions, with investigation on the selectivity of the metal capture process. The prepared materials were characterized using a suite of methods including FT-IR spectroscopy, X-ray powder diffraction (XRPD), thermogravimetric (TG) analysis, and N₂-adsorption/desorption analyses. The results showed that for Pb²⁺, the removal efficiency maximum (>99%) was independent of the intrinsic properties of the adsorbents, the initial concentration of Pb²⁺, and the co-presence of Cu²⁺. Conversely, the removal of Cu²⁺ was affected by the structural properties of the HAP adsorbents, d-HAP being the most efficient adsorbent for Cu²⁺ (93%). Immobilization of Pb²⁺ and Cu²⁺ onto HAP occurred by two different mechanisms: a dissolution–precipitation mechanism with formation of a Pb₁₀(PO₄)₆(OH)₂ phase was responsible for the Pb²⁺ uptake, whereas Cu²⁺ was immobilised by surface complexations involving Ca²⁺ species with carbonate and hydroxyl groups of HAP. In addition, leaching tests revealed that the confinement of the two metal species on HAP samples was permanent.