Environmental flow assessments (e-flows) are widely used within water allocation planning to address the threat to rivers and human communities posed by water extraction. However, conceptual models underpinning e-flows tend to include only biophysical interactions, eschewing socio-cultural complexity, local knowledge, and governance arrangements. These are critical where Indigenous people have strong connections with rivers and knowledge to contribute to planning. We used a transdisciplinary approach to develop a model of ecological values and a wider set of values held by Indigenous peoples in north-western Australia. Our model demonstrates the importance of hydrological connectivity for maintaining hydro-ecological values and Indigenous use for food and amenity and meeting religious responsibilities. We identified the need to recognize Indigenous and non-Indigenous governance and management systems at multiple scales to build legitimacy in e-flows and water planning. We propose guiding principles for using e-flows to protect aquatic ecosystems and their dependent human cultures and livelihoods.