The Greater Sydney Region coastline stretches from Newcastle to Wollongong and includes the metropolis of Sydney. It is the most populated section of Australia’s coastline and has a long history of urbanisation and industrialisation, but it also possesses a diverse range of habitats, stunning areas of naturalness and sections of coastline with low human populations. It is region where, like all of Australia, people value the coast for its environment, social, cultural and economic values. Protecting these multiple values in face of a wide range of threats requires solid evidence-based management. Doing so requires collaboration of managers, stakeholders, traditional owners, general public and researchers. Here, we describe an interview-based process to identify the major management issues and why research is needed; followed by negotiated dialogue to formulate potential research questions to address management needs and how the findings would be used by management; and finally an agreed prioritisation of the management issues and research projects. In this worked example, we outline the process used with NSW Government Aquatic Ecosystems Managers (Fisheries NSW). We outline the research priorities for the managers and the context for this prioritisation, and importantly assess the priorities in line with the NSW Threat and Risk Assessment and the Marine Estate Management Strategy. The prioritisation should provide guidance for NSW and Commonwealth government research agencies and university researchers who want to address key knowledge issues for management in the Greater Sydney Region. We hope this model will be useful to develop prioritised and targeted research in other regions around Australia.