Adequate sewage treatment is vital for maintaining New Zealand’s economy as well as offering economic and sustainable methods of treating wastewater globally. Effective treatment is required to protect both public health and the environment from anthropogenic activities. Pathogen removal mechanisms are largely unknown and are likely to be complex due to the diverse environment. The purpose of this study was the investigation of natural virus inactivation in waste stabilisation ponds. By investigating these complex mechanisms, particularly the enzymatic virus removal, we can develop models of pathogen removal and increase the knowledge of these processes to enable the efficient, low-cost, running of waste stabilisation ponds. A laboratory-scale waste stabilisation pond system was developed in order to investigate pathogen behaviour in the wastewater matrix. The laboratory-scale WSP system was combined with enzyme assays, viral enumeration, and genomic sequencing to investigate the bacterial communities present in wastewater and their potential production of enzymes involved in virus inactivation. It was determined that the bacterial communities in laboratory-scale and full-scale WSPs were compositionally similar, with a shared core microbiome. The bacterial abundance and functions associated with the bacteria varied in response to pond properties, while enzyme activity leads to reduced viral concentrations. Sequencing, physiochemical properties, and microbial pathogen reduction indicated a successful laboratory-scale WSP was developed. Human enteric virus concentration was reduced in the presence of extracellular enzymes present in wastewater, indicating a possible alternative for virus removal than expensive chlorination or UV.