The catchments, estuaries and near-shore marine zones of northern Australia contain high diversity with many unique and significant species and habitats including over 150 fish, 150 waterbird, 30 aquatic and semi-aquatic reptiles, and are critical in supporting productive fisheries and species of conservation significance. Globally, the development of water resources can lead to a range of impacts to the environment including changes in flow regimes, land-use change and changes to connectivity by building instream structures. In northern Australia, the problem is complicated by large spatial areas, diverse habitats and biota, and a developing knowledge base of ecology and flow needs. CSIRO, in collaboration with research partners, are undertaking work in three regions of northern Australia as part of an ongoing program of research to understand the risks and opportunities of water resource development. This talk will introduce the ecological methods for our analysis, and our approach to generating an ecological knowledge base to support the assessment water resource development across the diverse landscapes of northern Australia.