Indigenous peoples within the Murray–Darling Basin have traditionally struggled for the recognition of their cultural, social, environmental, spiritual, commercial and economic connection to the waters that they have traditionally used, as well as their right to engage in all stages of water planning processes. Despite Australian national and federal frameworks providing for the inclusion of Indigenous Australians’ objectives in planning frameworks, water plans have rarely addressed these objectives in water, or the strategies to achieve them. Indeed, insufficient resources, a lack of institutional capacity in both Indigenous communities and agencies and an inadequate understanding of Indigenous people's objectives in water management have limited the extent to which Indigenous objectives are addressed in water plans within the Murray–Darling Basin. In this context, the adoption of specific guidelines to meet Indigenous requirements in relation to basin water resources is crucial to support Indigenous engagement in water planning processes. Using insights from participatory planning methods and human rights frameworks, this article outlines a set of alternative and collaborative guidelines to improve Indigenous involvement in water planning and to promote sustainable and just water allocations.