Disinfection of Gram-negative bacterium Vibrio cholerae 569B in aqueous matrix by solar-photocatalysis mediated by Ag@ZnO core–shell structure nanocomposite particles was investigated. Silver nanoparticles are synthesized by the reduction of silver perchlorate followed by precipitation of zinc oxide shell and are employed in the photocatalytic disinfection of the model pathogen. Effect of photocatalyst loading and reaction temperature on the disinfection kinetics was studied. Disinfection efficiency in laboratory as well as real water samples was compared with that of pure-ZnO and TiO2 (Degussa P25). Nanocomposite system has shown optimum disinfection (≈98%) at 40–60min of sun-light exposure with a catalyst loading of 0.5mg/L of the reaction solution. The reduction of aquatic bacterial densities by photocatalytically active Ag@ZnO core–shell nanocomposite in presence of natural sun-light may have potential ex situ application in water decontamination at ambient conditions.