Northern Australia covers vast and diverse landscapes comprising largely public and Indigenous tenures. Long-term Aboriginal and pastoral management, isolation and a challenging terrain and climate have shaped a landscape of national, if not international, conservation value. Northern Australia, however, also has a fragile economy, and there is tension amongst Indigenous, economic and conservation interests. Managed poorly, emerging conflicts could damage the real opportunities that each presents, resulting in major land and natural resource-use conflicts or unsustainable development. As healthy governance systems are the key to effective natural resource management (NRM), this paper presents a preliminary exploration of the health of NRM governance across Northern Australia, with a focus on the catchment scale. We analysed three focal catchments; the Fitzroy in the Kimberley region of Western Australia, the Daly in the top end of the Northern Territory and the Gilbert in north-western Queensland. We find that the governance of each catchment has different strengths and weaknesses depending on history and context. Common challenges, however, include shifting national and state/territory policy frameworks, fragmented funding of science and limited consensus building via spatial decision support. From this analysis, we explore potential reforms in catchment governance across this increasingly contested landscape.