When amphibians are brought into an amphibian facility, every precaution should be taken to prevent the introduction of diseases, including testing for chytrid fungus Batrachochytriumdendrobatidis. Equal consideration is recommended for the disinfection of waste products, including water, to prevent the spread of disease both within and between facilities, and to complete the biosecurity cycle. The disinfection of all waste products is particularly important when the facility houses amphibians from remote locations. This report describes an automated waste-water disinfection system (AWWDS) to disinfect waste water from amphibian enclosures and research facilities. The AWWDS is reliable as it does not rely on an individual's compliance to dosing protocols and it is economical because it reduces labour time. The AWWDS also provides an efficient infrastructure to disinfect the amounts of water produced by a moderate-sized busy amphibian captive-breeding and research facility.