In this paper, the removal of noble and non-noble metals from aqueous solutions on multi-dimensional hydroxyapatite microspheres (MD-HAp-Ms) in column experiments was studied. The efficiency of non-noble metal removal, viz. Co(II) and Ni(II) commonly presented in the environment, and the attachment mechanism onto MD-HAp-Ms readily depended on the concentration of H+ in the influent solution. In contrast, ICP-MS, SEM, XRD, TEM/EDX and RAMAN investigations independently revealed that the adsorption of Pb(II) onto the minicolumns was complete over the entire pH range and did not significantly depend on the medium acidity/basicity. The formation of a hydroxylpyromorphite phase with a general formula of Pb5-x/Cax(PO4)3OH onto the calcium MD-HAp-Ms minicolumns during Pb(II) uptake regardless from the used pH range was detected. Compared to non-noble metals, the noble ions Ag+, Pd2+, Pt2+, Au3+ formed nanoparticles with an average size of 10–50 nm during adsorption onto the MD-HAp-Ms in ammoniacal medium. The efficiency of noble ions removal was in accordance with their standard electrode potential (E0).