Hospital wastewaters can become a route for dissemination of antibiotic-resistant bacteria to the environment if not properly treated. Some of these bacteria are able to survive conventional disinfection treatments (e.g. chlorination, UV irradiation), which evokes the need for novel disinfection methods. The metal-exchanged zeolites were tested as novel antibacterial agents for wastewater treatment. The natural zeolite clinoptilolite enriched with silver (AgNZ) showed far better antibacterial activity towards hospital pathogenic bacterium Acinetobacter baumannii when compared with copper-exchanged zeolite (CuNZ), with minimal bactericidal concentration of 0.25–2 (AgNZ) compared with 32–64 mg L−1 (CuNZ) in a batch system and respective log 5.6 reduction compared with log 0.5 reduction in a flow system with pure bacterial culture. In the flow system with real effluent wastewater from the treatment plant, the removal of carbapenem-resistant bacteria using AgNZ was 90%–100% during the 4 days of the experimental run. These results indicate that the AgNZ efficiently removes pathogenic bacteria from the wastewater, including A. baumannii, and is promising as a disinfectant material in a bead filter system.