Sustainable water resource planning in northern Australia requires informed aquatic ecological input in order to determine the potential environmental impact. However, an absence of complete ecological knowledge inevitably confounds the process. Incomplete ecological knowledge and understanding is pronounced in parts of northern Australia as a function of the remoteness and a reduced scientific legacy relative to more developed parts of the continent. This presentation describes efforts to conceptualise and model fish responses to potential water resource development and particularly changes in flow regime and connectivity as a consequence of potential dams and water harvesting. Three phases of analyses were implemented: formulation of conceptual model narratives, hydrometric analysis and a preference curve approach. This approach proved informative for exploring a range of scenarios incorporating both development and climate change scenario. The application is used to explore broader themes of incomplete knowledge in the context of fish, considering flagship species and biodiversity indicator species and functional groups of species in the context of water resource planning. We demonstrate this using catchments distributed across northern Australia.