The influence of silver ions on antibacterial properties and morphology of Hydroxyapatite-Ag (HА-Ag) and Hydroxyapatite-Alginate-Ag (HA-Alg-Ag) nanocomposites was studied. The microstructure and phase composition of the obtained nanocomposites were investigated by SEM, TEM, XRD, FTIR methods, and the formation of the crystalline phase of Ag3PO4 was proved. According to the results, silver ions were incorporated into the HA structure, partially replacing calcium ions. The antimicrobial activity assessment was carried out on Gram-negative (Pseudomonas aeruginosa) and Gram-positive bacteria (Staphylococcus aureus) test cultures by the co-incubation and modified «agar diffusion» methods. We have demonstrated that antimicrobial and adhesive properties of both Ag-HA and HA-Alg-Ag are strongly affected by the crystal lattice structure, controlled by silver ions location. The composite materials could be of great interest in the biomedical field, including the design of coatings that prevent or lag the bacterial biofilm development.