Indigenous Research Methodologies (IRMs) for considering cultural values of water are a missing component of water and wetlands management in Australia. On this dry, flat and ancient continent Traditional Knowledge has been passed on from generation to generation for millennia. The profound knowledge of surface and groundwater has been critical to ensuring the survival of Indigenous peoples in the driest inhabited continent, through finding, re-finding and protecting water. Indigenous Research Methodologies can provide a basis for the exploration of this knowledge in a way that that is culturally appropriate, and which generates a culturally safe space for Indigenous researchers and communities. The development of IRMs has been and continues to be limited in Australia in the water context, primarily due to the lack of Indigenous water practitioners, with non-Indigenous researchers dominating the sector. The intention of the paper is to shift and decolonise the research paradigm from studying Indigenous peoples through non-Indigenous research methodologies, to partnering in developing methods appropriate to Indigenous knowledge systems. Indigenous Research Methodologies are rooted in Indigenous epistemologies and ontologies and represent a radical departure from more positivist forms of research (Wilson, Can J Native Educ 25:2, 2001). This allows the Indigenous researcher to derive the terms, questions, and priorities of what is being researched, how the community is engaged, and how the research is delivered. This paper provides an overview of Indigenous engagement in water management in Australia and Aotearoa (New Zealand), with reference to case studies. These more general models are used as the basis for developing an IRM appropriate to the Kamilaroi people in the Gwydir Wetlands of northern NSW, Australia.