There are many proposed and ongoing commercial, industrial, and residential developments within the Darwin Harbour catchment in Northern Australia, to accommodate the projected population growth over the next 20 years. Hence, it is necessary to ensure the balance between these developments and ecosystem conservation. We evaluated ecological risk for the Darwin Harbour using a relative risk model (RRM). The catchment was divided into 22 risk regions based on small catchment boundaries and their homogeneity. Through the RRM, we ranked and summed the stressors and habitats within regions. The interaction between stressors and habitats were modeled through exposure and effect filters. The ecological assessment endpoints were maintenance of the mangrove health and the maintenance of water quality. The risk regions—Myrmidon Creek, Blackmore River, Bleesers Creek, and Elizabeth River—showed the highest total relative risk for ecological assets. These risk regions had a high percentage cover of industrial, commercial, and residential areas; diffuse entry points; and climate change effects. Creek A, Sandy Creek, West Arm, and Pioneer Creek were the risk regions with lowest total relative risk scores. The RRM is a robust application that is suitable for a large geographic area where multiple stressors are of concern.