The purpose of this study was to investigate the possibility of using zinc oxide nanoparticles (ZnONPs) instead of silver nanoparticles (AgNPs) for removing Aeromonas hydrophila from water used to culture Cyprinus carpio juvenile. Antibacterial materials as filter media were prepared by coating ZnONPs (two coating methods, referred as ZnA and ZnB) or AgNPs (referred as Ag) on the porous surfaces of zeolite beads. The characterization of coated samples was determined using FESEM, EDS, and GFAAS. The antibacterial activities of prepared samples were evaluated by the zone of inhibition test, tube test, and flow test. The diameter of inhibitory zones formed by ZnONP- and AgNP-coated zeolite beads was significantly higher than uncoated zeolite (control) (P < 0.05). Also, the tube test results revealed 100% killing of the bacterial cells after 24 h of contact to all coated materials. In the flow test (without fish), the antibacterial efficiency of filter columns that contained ZnA, ZnB, and Ag found to be 34.84, 23.77, and 100% after 96 h, respectively. The mortality rate of carp juveniles cultured in infected water treated with AgNP filters was significantly lower than those cultured in infected water or treated with ZnONPs filters (P < 0.05). The results indicated that although ZnONP filter media have somewhat antimicrobial properties (especially in vitro), their ability to complete removal of microorganisms from the water is not as high as AgNP filters. So, it still seems that zeolite coated with AgNPs has a higher potential for water disinfection in aquaculture.