Phylogeographic structure in freshwater species is a consequence of physical changes to aquatic connectivity over long periods of time, current patterns of hydrologic connectivity and flow regime, and traits of the species relevant to dispersal and range expansion. Many presently distinct river systems in northern Australia were connected at various times during Pleistocene glacial cycles by the ancient Lake Carpentaria, whilst rivers in the Kimberley region of northwestern Australia have long been isolated systems. Furthermore, variation in landscape topography in northern Australia has lead to the evolution of highly disjunct floodplain wetlands and disjunct, albeit widespread, distribution in some wetland-associated fish. Present-day monsoonal ecology (i.e. seasonal fluctuation between extremely wet, high flow and dry, low flow conditions) of riverine systems in northern Australia is also likely an important determinant of phylogeographic patterns in aquatic biota. Using mitochondrial and nuclear DNA sequence data, we test phylogeographic hypotheses concerning past and present landscape attributes on patterns of genetic variation in several continuously distributed freshwater fish species and three species with highly disjunct distributional ranges in northern Australia.