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Coastal wetlands and waterways are important for biodiversity conservation and ecosystem services. Many have been under threat from land clearing, infill development and, increasingly, to sea level rise. Such wetlands not only need to be conserved at their present locations, they must be also able to retreat landwards if ecological functionality and resilience are to be maintained. While land use planning processes and applications can provide a structured approach for both in situ conservation and preservation of retreat pathways, rarely have these outcomes been achieved. This paper documents the development of GIS-based State-wide wetlands and waterways and coastal refugia planning overlays in Tasmania, south-eastern Australia, for inclusion within the new State-wide planning system. The overlays were designed to conserve current wetland extent, their buffers and future retreat areas. Through this case study, we describe and discuss the important technical, procedural and socio-political requirements for effective wetlands protection overlay development, application, monitoring and revision. The overlays provide a useful planning tool for evaluating how best to accommodate wetland conservation. We recognise, though, that planning processes will always entail trading-off development benefits, social costs, and environmental impacts within a context of increasing socio-political awareness of the functions, benefits and ecosystem services of wetlands and waterways.