Addressing environmental problems in estuaries is a worldwide problem. Establishing benchmarks and targets for management is critical, whether the aim is conservation, restoration or sustainable use. Palaeoecological techniques have rapidly improved during the past decade, particularly with advances in methods that allow high resolution quantitative assessments of environmental change. Palaeoecology is a useful tool in environmental management as it allows pre-impact conditions, the rate, extent, direction and cause of change, and range of natural variability to be determined. Australian estuarine ecosystems are qualitatively different from the often more well-studied estuaries in North America and Europe, which means site-specific studies of Australian estuaries are needed to inform management. While a potentially useful and valuable tool, palaeoecological techniques have not yet been widely adopted and practically implemented as part of estuarine management strategies and policy frameworks in Australia. We discuss the role palaeoecological techniques have to play in estuarine management by providing two case studies undertaken in Australia that have provided management information. We aim to encourage communication and dialogue between scientists and environmental managers about the potential for widespread practical adoption and implementation of palaeoecological techniques into Australian estuarine science, management and policy frameworks.