Seagrass habitats play a critical ecological and cultural role across northern Australia, supporting carbon sequestration and providing essential nursery and foraging grounds for marine fauna. Our understanding of this ecosystem is limited by the region’s remoteness, sparse historical data, harsh environmental conditions, and associated safety concerns; however, these knowledge gaps can be addressed through habitat suitability modelling. In this study we compiled existing environmental spatial layers to model seagrass habitat suitability in this data-poor region. Northern Australia presents substantial limitations for predictive modelling due to the lack of high spatial and temporal resolution environmental data, in comparison to more populated areas with high resolution environmental datasets. To further understand seagrass distribution in this area, we applied random forest modelling to identify the environmental conditions most strongly associated with seagrass occurrence from Shark Bay to the Torres Strait. The resulting habitat probability model produced the first broad-scale predictive map of seagrass distribution across northern Australia. This map highlights priority areas for future surveys, identifies locations where seagrass may have historically persisted but has succumbed to anthropogenic pressures, and provides a spatial tool to support Traditional Owners with Sea Country planning, guiding management interventions and enhancing protection of these significant habitats.