This study focuses on coastal management issues relevant to key decision-makers in Australia's Northern Territory with respect to growing concerns about the effects of sea level rise on coastal freshwater wetlands. There is a growing global knowledge base and understanding of the symbiotic relationship between ecological forms of coastal protection and benefits to both small- and large-scale anthro-natural systems. This work summarises, and then provides a new scoring/ranking system for, the range of traditional and modern eco-engineering options available in terms of their effectiveness at addressing the concerns of stakeholders in the future. Considering the evidence that the Mary River is already showing signs of adaptation and that the coastal wetlands in this area are relatively pristine compared to most coastal wetlands around the world, there is a positive outlook. The opportunity to use natural wetland processes without significant cost or land management burden should be harnessed with planning in place to prepare for the effects of sea level rise. In the case of the Mary River wetlands, traditional engineering is neither required, nor beneficial; ecological engineering associated with conservation and rehabilitation is deemed as the more effective management response.