Most Australian jurisdictions, including Queensland, have struggled to sufficiently incorporate Indigenous values into their institutional frameworks. As a result, opportunities for formal Indigenous participation in water governance remain scarce. This study sought to fill a gap in knowledge through a qualitative exploration of Aboriginal water values in south east Queensland (SEQ). It explored how Traditional Custodians value SEQ waterways and how understanding these values can assist managers to adequately integrate Indigenous interests into water management and policy. Twenty Traditional Custodians, from across the SEQ region, participated in either a focus group with others from their Custodial group, or an individual interview (a choice was offered). Analysis was according to Kellert’s typology of values. The research shows that Traditional Custodians’ values towards estuarine and marine waterways in SEQ are multi-dimensional. Indigenous cultural values of water encompass more than spiritual and customary objectives, and extend beyond cultural heritage paradigms. Aesthetic values were strongly associated with ecosystem health, a point of difference from studies of non-Indigenous values towards water. As expected, identity is closely associated with the values and so a strong sense of personal loss was associated with damaged waterways. Understanding people’s connections with waterways will help managers to engage and partner more effectively with Indigenous people, and to integrate social dimensions in their future management of waterways.