The northern Australian coastline supports ecologically significant seagrass ecosystems that play a vital role in marine biodiversity and carbon sequestration, and that are culturally significant to Australia’s First Nations peoples. Seagrass ecosystems sustain marine megaherbivores, fish assemblages, and broader coastal resilience. Despite extensive seagrass research in Australia, historical spatial data remains fragmented, poorly curated, and rarely publicly accessible. To address this gap, we have compiled, validated, and synthesised historical seagrass spatial data from 1879 to 2023 along the Western Australian and Northern Territory coastlines. This dataset includes geolocated seagrass presence/absence records, data on 15 seagrass species, substrate type, depth, and collection dates. Our dataset comprises over 147,000 data points and more than 500 seagrass polygons, spanning from Shark Bay, Western Australia, to the Northern Territory/Queensland border. This spatial resource builds on previous seagrass data syntheses for the Gulf of Carpentaria, Torres Strait and the Great Barrier Reef and provides a critical baseline for predictive modelling, identifies biologically important areas, and highlights data-deficient regions where future research efforts should be prioritised across northern Australia.