The Wet/Dry Tropics of Northern Australia is one of the few global regions where relatively low anthropogenic impacts on freshwater biodiversity occur. However, the understanding of faunal diversity patterns, particularly for macroinvertebrates is low. The objective of this work was to examine the patterns and processes affecting macroinvertebrate biodiversity across the region. To do this we combined our studies of aquatic macroinvertebrate assemblages in the region with information from the Atlas of Living Australia (ALA) and studies described in Northern Territory and Commonwealth government reports. We found a latitudinal pattern with higher diversity in the north compared with the south, largely driven by the higher rainfall in the northernmost catchments. Larger catchments also supported higher diversity. A significant proportion (approximately 30%) of the macroinvertebrate species recorded are undescribed. This highlights the need for greater taxonomic effort to be applied to the fauna of this region, to ensure that new species are recognised, and distributions are accurately recorded. Our findings provide a baseline against which assessments of ecological change over time, including those in response to human activities, can be made. This is particularly important because the pressures on freshwater systems are increasing as developments in the region expand. These include hydraulic fracturing (fracking) for shale gas and intensive agriculture, including cotton. Our findings will inform the preparation of water allocation plans, freshwater conservation strategies and monitoring programs.