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As the health of many coastal ecosystems declines, there is an increasingly urgent need for research that transcends academic disciplines and can respond to complex environmental problems. While the benefits of transdisciplinary research are widely recognised, there are institutional and practical constraints on researchers wishing to put these approaches into practice. In this paper we seek to understand how incorporating participatory elements into research design and data collection can enhance the benefits of a transdisciplinary approach and improve outcomes for scientists and users of research. To do so, we describe and reflect on a transdisciplinary research project conducted in a large industrial port in the Great Barrier Reef World Heritage Area, Australia. Drawing on experiential observation and theoretical contributions from across the literatures on transdisciplinary and participatory research, we also develop an integrated research framework that can be applied across contexts. The research demonstrates that incorporating participatory techniques during the research scoping phase can help researchers to develop a transdisciplinary research programme that can both strengthen research outcomes and ensure their relevance to coastal communities and decision makers.