The Relative Risk Model (RRM) was used to undertake a spatially explicit regional ecological risk assessment at a continental scale for the 1.1 million km2 Northern Tropical Rivers (NTR) region of Australia, and at a catchment scale for the Daly River, Northern Territory. The NTR RRM assessed risks of 18 threats to three aquatic habitats and four ecological assessment endpoints across 51 catchments, while the Daly River RRM assessed risks of 17 threats to three aquatic habitats and five ecological assessment endpoints across 18 sub-catchments. The three most significant current threats to the aquatic ecological assets for the NTR region were cattle grazing on native vegetation, feral pigs, and unmanaged fire, and those for the Daly River catchment were cattle grazing on native vegetation, transport/communications infrastructure, and land clearing. Climate change and associated sea-level rise are emerging problems that threaten to cause much greater impacts than currently exist. The uncertainties associated with both scales of assessment were considerable and are discussed. Despite the uncertainties the RRM was found to be a robust method for assessing and prioritising the risks of multiple threats to multiple assets and is a useful screening tool for decision-makers in prioritizing research and/or management actions.