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The Great Barrier Reef World Heritage Area (GBRWHA) in north eastern Australia spans 2500 km of coastline and covers an area of ~ 350,000 km2. It includes one of the world's largest seagrass resources. To provide a foundation to monitor, establish trends and manage the protection of seagrass meadows in the GBRWHA we quantified potential seagrass community extent using six random forest models that include environmental data and seagrass sampling history. We identified 88,331 km2 of potential seagrass habitat in intertidal and subtidal areas: 1111 km2 in estuaries, 16,276 km2 in coastal areas, and 70,934 km2 in reef areas. Thirty-six seagrass community types were defined by species assemblages within these habitat types using multivariate regression tree models. We show that the structure, location and distribution of the seagrass communities is the result of complex environmental interactions. These environmental conditions include depth, tidal exposure, latitude, current speed, benthic light, proportion of mud in the sediment, water type, water temperature, salinity, and wind speed. Our analysis will underpin spatial planning, can be used in the design of monitoring programs to represent the diversity of seagrass communities and will facilitate our understanding of environmental risk to these habitats. [ABSTRACT FROM AUTHOR]