Due to the antibacterial characteristics, numerous-growing applications of silver nanoparticles (AgNPs) and its coated forms impact water treatment by ozone. The influence of ozone on the aggregation of bare AgNPs and polyvinylpyrrolidone-capped form (PVP-AgNPs) was investigated, as toxicity of NPs depends on particle aggregation/surface charge. Full factorial experimental design was employed to investigate the impact of pH, concentration of NPs' suspension, and ozonation time on bare and PVP-capped AgNPs. Z-Average, zeta potential, and polydispersity index (PdI) of NPs were measured as aggregation criteria. The most effective variables on aggregation of NPs were the coating layer (40-75.5% contribution), pH (14.1-29.6% contribution), and ozonation time (6.5-10.1% contribution), respectively. The aggregation rate increased with increasing ozonation time and decreased with pH. The aggregation of ozonated AgNPs (Z-average up to ~ 4000 nm) was much greater than that of ozonated PVP-AgNPs (Z-average up to ~ 450 nm) due to interaction of ozone-PVP stabilizing layer. During ozonation, the PVP-AgNPs' surface charge shifted from - 6.62 (steric repulsion) to - 29.17 mV (electrosteric repulsion) at pH 7.5, thereby requiring more treatment time to aggregate compared with AgNPs. Graphical abstract.