Studies that apply indigenous ecological knowledge to contemporary resource management problems are increasing globally; however, few of these studies have contributed to environmental water management. We interviewed three indigenous landowning groups in a tropical Australian catchment subject to increasing water resource development pressure and trialed tools to integrate indigenous and scientific knowledge of the biology and ecology of freshwater fish to assess their water requirements. The differences, similarities, and complementarities between the knowledge of fish held by indigenous people and scientists are discussed in the context of the changing socioeconomic circumstances experienced by indigenous communities of north Australia. In addition to eliciting indigenous knowledge that confirmed field fish survey results, the approach generated knowledge that was new to both science and indigenous participants, respectively. Indigenous knowledge influenced (1) the conceptual models developed by scientists to understand the flow ecology and (2) the structure of risk assessment tools designed to understand the vulnerability of particular fish to low-flow scenarios.