This study evaluated the effect of natural water composition onto the bactericidal and physicochemical properties of silver nanoparticles (AgNPs) stabilized with three different polymeric compounds. All the nanoparticles behaved similarly in the water conditions tested. Compared to solutions with low organic matter content and monovalent ions, lower disinfection performances of AgNPs suspensions were obtained in the following order seawater ≤ high organic matter content water ≤ high divalent cations content synthetic water. Suspension of AgNPs in seawater and water with divalent cations (Ca(2+) and Mg(2+)) formed larger AgNPs aggregates (less than 1400 nm) compared to other solutions tested (up to approximately 38 nm). The critical coagulation concentration (CCC) of AgNPs was determined to quantitatively evaluate the stability of the nanoparticle suspension in different water conditions. When the concentration of dissolved organic matter was increased from 0 mg/L to 5 mg/L, the CCC increased by a factor in the range of 2.19 ± 0.25 for all AgNPs in divalent solutions, but a smaller increase occurred, in the range of 1.54 ± 0.21 fold, when monovalent solutions were used. The concentration of ionic silver released indicated that the dissolved Ag(+) (3.6-48.2 ppb) was less than 0.5% of the total mass of Ag(0) added. At all the conditions tested, the concentration of silver ions in solution had a negligible contribution to the overall anti-bacterial performance of AgNPs. This study demonstrated that the anti-bacterial performance of AgNPs at selected natural water conditions decreases in the presence of dissolved natural organic matter or divalent ions, such as humic acid and calcium carbonate. These results may be helpful in understanding the toxicity of AgNP in various natural water conditions and in explaining the risk associated with discharging AgNP in natural aquatic systems.