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Carboxymethyl starch (CMS) and carboxymethyl cellulose (CMC) loaded by highly dispersed metal subnanoparticles (MSNPs) showed antibacterial activity against E. coli and B. subtilis strains. Copper and silver were found to act in both cationic and zero-valence forms. The antibacterial activity depends on the metal species content but only up to a certain level. Silver cation (Ag+) showed higher antibacterial activity as compared to Ag0, which was, however, more effective than Cu0, due to weaker retention. The number of carboxyl groups of the biopolymers was found to govern the material dispersion in aqueous media, the metal retention strength and dispersion in the host-matrices. Cation and metal retention in both biopolymers was found to involve interactions with the oxygen atoms of both hydroxyl and carboxyl groups. There exists a ternary interdependence between the Zeta potential (ZP), pH induced by the biocidal agent and its particle size (PS). This interdependence is a key factor in the exchange processes with the surrounding species, including bacteria. Clay mineral incorporation was found to mitigate material dispersion, due to detrimental competitive clay:polymer interaction. This knowledge advancement opens promising prospects for manufacturing metal-loaded materials for biomedical applications.