Summary Indigenous ecological knowledge can inform contemporary water management activities including water allocation planning. This paper draws on results obtained from a 3-year study to reveal the connection between Indigenous socio-economic values and river flows in the Daly River, Northern Territory. Qualitative phenological knowledge was analysed and compared to quantitative resource-use data, obtained through a large household survey of Indigenous harvesting and fishing effort. A more complete picture of Indigenous resource-use and management strategies was found to be provided by the adoption of mixed methods. The quantitative data revealed resource-use patterns including when and where species are harvested. The qualitative Indigenous ecological data validated results from the quantitative surveys and provided insights into harvesting and resource management strategies not revealed by the discrete time-bound surveys. As such, it informed the scientific understanding of patterns of resource use and relationships between people, subsistence use and river flows in the Daly River catchment. We recommend that natural resource managers, researchers and Indigenous experts prioritise collaborative projects that record Indigenous knowledge to improve water managers’ understanding of Indigenous customary aquatic resource use.