The Gulf of Carpentaria and Torres Strait in north-eastern Australia support globally significant seagrass ecosystems that underpin fishing and cultural heritage of the region. Reliable data on seagrass distribution are critical to understanding how these ecosystems are changing, while managing for resilience. Spatial data on seagrass have been collected since the early 1980s, but the early data were poorly curated. Some was not publicly available, and some already lost. We validated and synthesized historical seagrass spatial data to create a publicly available database. We include a site layer of 48,612 geolocated data points including information on seagrass presence/absence, sediment, collection date, and data custodian. We include a polygon layer with 641 individual seagrass meadows. Thirteen seagrass species are identified in depths ranging from intertidal to 38 m below mean sea level. Our synthesis includes scientific survey data from 1983 to 2022 and provides an important evidence base for marine resource management.