The colonization of poly(methyl methacrylate) (PMMA) denture base materials by pathogenic microorganisms is a major problem associated with the use of prostheses, and the incorporation of antimicrobial fillers is a method of improving the antimicrobial properties of these materials. Numerous studies have demonstrated the initial in vitro antimicrobial effectiveness of this type of material; however, reports demonstrating the stability of these fillers over longer periods are not available. In this study, silver sodium hydrogen zirconium phosphate was introduced into the powder component of a PMMA denture base material at concentrations of 0.25%, 0.5%, 1%, 2%, 4%, and 8% (w/w). The survival rates of the gram-positive bacterium Staphylococcus aureus, gram-negative bacterium Escherichia coli and yeast-type fungus Candida albicans were established after fungal or bacterial suspensions were incubated with samples that had been previously stored in distilled water. Storage over a three-month period led to the progressive reduction of the initial antimicrobial properties. The results of this study suggest that additional microbiological tests should be conducted for materials that are treated with antimicrobial fillers and intended for long-term use. Future long-term studies of the migration of silver ions from the polymer matrix and the influence of different media on this ion emission are required.