Australia’s ability to address Indigenous claims for water rights and to advance both national Indigenous and water policy is hampered by a lack of information on Indigenous water entitlements and the communities that hold them. This paper contributes to the policy agenda of increasing Indigenous water rights by developing a method that quantifies and enables spatially explicit comparison of Indigenous-held water within and across Murray-Darling Basin jurisdictions. We construct baselines for (i) Indigenous population (ii) Indigenous holdings of surface water entitlements, and (iii) Indigenous holdings of groundwater entitlements across water management units in the Basin. We estimate that Indigenous surface water holdings constitute no more than 0.17% of the equivalent permitted take across the entire Basin. Groundwater entitlements held by Indigenous entities constitute 0.02% of all available groundwater. The approximate market value of these water entitlements is A$19.2 million in 2015–16 terms, which equates to 0.12% of the total $16.5 billion market value. In contrast, 5.3% of the Murray-Darling Basin population is Indigenous, a proportion that is rapidly increasing. The production of estimates of this type, and Indigenous control of the data needed to generate them, are first steps in a reparations process that can contribute towards Indigenous water justice.