Yolŋu Aboriginal people’s knowledge about water (‘gapu’) and its governance has strong cultural significance and meaning in East Arnhem Land Aboriginal worlds in northern Australia. This study used transdisciplinary research methods to explore the ways in which Yolŋu Aboriginal gapu and Western science hydrological knowledge can work together and contribute towards water management on Milingimbi Island, a small, resource-constrained, bedrock island. Transcending disciplinary boundaries is distinctly different to an interdisciplinary, socio-hydrological perspective, which can pose a risk to hybridising Aboriginal knowledge and Western science. Community engagement activities and workshops were conducted as part of a three-year research project to bring together the incommensurable knowledge communities. A participatory three-dimensional mapping exercise created a shared space, facilitating an open-dialogue exchange of insight and knowledge between Aboriginal knowledge authorities, hydrologists, public servants, and academic researchers. This paper prompts readers to reconsider the ways water can be perceived and conserved in a post-colonial context.