Northern Australia hosts two-thirds of the Australian freshwater fish fauna and most of the unexplored diversity. Despite relatively low levels of development, there are significant pressures and a desire to avoid repeating management mistakes of more developed catchments. Exotic and translocated native fishes pose a significant threat to this biodiversity, even in relatively unimpacted catchments. Two new projects are exploring this native diversity and the increasing threat of pest fish invasions. The first is “A Comprehensive Analysis of Freshwater Fish Faunas of Northern Australia and Their Key Management Needs”. This project aims to database the recorded distribution of all freshwater fishes across northern Australia; to identify and fill gaps in field survey effort; undertake a genetic and taxonomic revision of terapontid grunters; and to produce a website portal for this information. The second is “Integrated Management of Tilapia and Other Exotic and Native Pest Fishes in NE Queensland”. This region hosts 19 exotic and 36 translocated native fish species, with the rate of new range incursions, especially for exotic species, increasing rapidly. This project covers public education; field survey to delineate pest fish distribution; research into impacts of tilapia; and developing control actions to limit tilapia establishment and dominance.