Marra Sea Country in the southwestern Gulf of Carpentaria includes diverse ecosystems that are ecologically, economically, and culturally significant, yet understudied. The Limmen Bight Marine Park (Northern Territory) and Limmen Marine Park (Commonwealth) overlap Marra Sea Country and aim to protect ecosystems and culturally significant areas and sustainably manage fishing and tourism. Research and monitoring partnerships that identify changes in habitats and biodiversity are crucial to achieving these goals. li-Anthawirriyarra Rangers, JCU and CDU researchers, NT Parks, and Parks Australia have partnered to map Marra Sea Country’s marine habitats and fish communities. Baited remote underwater video stations (BRUVs) captured diverse and distinct fish communities associated with habitats including seagrass, soft coral, and bare sediment inside and outside the marine parks. Species richness was greatest in seagrass and soft coral habitats. Seascape connectivity impacts fish community dynamics and ontogenetic shifts between habitats. This interagency partnership is producing vital spatial data that will inform Sea Country planning and management of these important ecosystems by supporting Traditional Owners and governments in making evidence-based decisions to protect cultural and ecological values. By combining Indigenous and scientific knowledge, this partnership strengthens collaborative management of Marra Sea Country.