Freshwater ecosystems across northern Australia are significant places for Indigenous communities as food and drinking water sources, as well as cultural and recreation sites. Feral ungulates, including Asian water buffalo (Bubalus bubalis) and pigs (Sus scrofa), are prevalent throughout The Top End of the Northern Territory and, due to their foraging and wallowing behaviors, they increase the turbidity of waters and excrete zoonotic organisms that are pathogenic to humans. Cryptosporidium and Giardia are the most common cause of waterborne gastroenteritis throughout the world. They are transmitted via the faecal-oral route, through contact with other people, animals, water, food and contaminated environments. When compared with other developed countries with similar surveillance systems, Australia has the second highest reports of cryptosporidiosis, after New Zealand. Reported rates of cryptosporidiosis in Australia share distinct geographic and demographic patterns in favour of warm, remote areas with high Indigenous populations. Giardia is also disproportionately represented in remote Indigenous populations. The aim of this study is to build a cross cultural knowledge base of the environmental impacts and health implications of sharing freshwater ecosystems with feral ungulates, via the use of local Indigenous Knowledge and Western Science techniques around the remote Aboriginal community, Ngukurr in the Northern Territory. The research involves interviews with local elders to understand perceptions of threats and how people assess water quality and safety. It involves microbial source tracing methods using PCR and DNA sequencing, which uses molecular characterisation to determine species specific and sensitive microbes making is possible to attribute microbial species to a host source and determine zoonotic potential. Considering the disproportionate representation of enteric disease in remote Aboriginal communities from the Northern Territory, determining the potential role of billabongs in environmental disease transmission will be valuable for Aboriginal communities across Northern Australia.