Australia's national water policy represents a substantial change from the previous approach, because it recognises a potential need for allocations to meet particular indigenous requirements, which will have to be quantitatively defined in water allocation plans. However, indigenous values associated with rivers and water are presently poorly understood by decision-makers, and Indigenous priorities are rarely reflected in allocation decisions. This article describes the range of Australian indigenous values associated with water, and the way they have been defined in contemporary water resource policy and discourse. It argues that the heavy reliance of indigenous values on healthy river systems indicates that, theoretically at least, they are logically suited for consideration in environmental flow assessments. Yet in practice they have tended to be overlooked in a scientific process that leaves little room for different world views relating to nature, intangible environmental qualities and human relationships with river systems that are not readily amenable to quantification. There is often an implicit but untested assumption that indigenous interests will be protected through the provision of environmental flows to meet aquatic ecosystem requirements, but the South African and New Zealand approaches to environmental flow assessment, for example, demonstrate different cultural perspectives and subsistence uses can potentially be accommodated. Debate with indigenous land-holders and experimentation will show how suited different environment flow assessment techniques are to addressing indigenous environmental philosophies and values, but in the meantime environmental water managers should develop more inclusive processes and prioritise indigenous water management objectives in their management programs and water purchases.