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. Water is limited in many places, and it must be carefully managed for many different needs. Indigenous people rely on rivers for food, amenities, and to meet spiritual responsibilities, but they can be overlooked when water management plans are being developed. This study looks at the Fitzroy River in northern Australia and how decisions about water use can affect both Indigenous people who live there and the local biodiversity. This information was used to create guidelines for more inclusive water planning. These include encouraging government decision makers to have earlier and more effective dialogue with Indigenous peoples; recognize the rights, values, governance, and management systems of Indigenous peoples; and use both scientific and Indigenous knowledge when considering the water needs of biodiversity. These tools are being used in northern Australia and can be used in other locations to help protect rivers and their dependent human cultures and livelihoods. Water use has fundamentally altered rivers globally. Indigenous people rely on rivers for food, amenities, and spiritual responsibilities, but these needs are rarely included in water management planning. This study looks at how water use can affect Indigenous people and biodiversity in northern Australia. We used this information to create guiding principles for more inclusive water planning. These are being used in northern Australia and can be adapted to help protect rivers and their dependent human cultures and livelihoods elsewhere.