Using a 30 metre resolution and a modelled predicted probability of >0.2 we identified 88,331 km2 of potential seagrass habitat in the Great Barrier Reef lagoon (GBR); 1,111 km2 in estuaries, 16,276 km2 in coastal areas, and 70,934 km2 in reef areas. 36 seagrass community types were defined by species assemblages. The environmental conditions that structured the location and extent of these communities included depth, tidal exposure, latitude, current speed, benthic light, proportion of mud, water type, water temperature, salinity, and wind speed. Environmental parameters interact with the topography of the reef and changes in the coastal plain, its watersheds, and with latitude. We describe seagrass distributions and communities that are shaped by multiple combinations of these environmental conditions. We show that the structure, location and distribution of the seagrass communities in the GBR is the result of complex interactions. Understanding this and how it overlays with the location of jurisdictions and monitoring and assessment programs can guide management in interpreting trends, understanding risks and in developing suitable responses.