Indigenous knowledge systems (IKSs) can, and do, contribute to natural resource management (NRM) in Australia and elsewhere. However, cross-cultural NRM and scientific research usually emphasizes particular components of IKSs, rather than engaging with the value of an integrated complex IKS. Focusing on two case studies of Aboriginal groups in the Kimberley region of northwestern Australia, we present a conceptual framework that represents how IKSs can manifest as a system of wetland management. The framework depicts how beliefs, knowledge, and practices are inter-related, forming a meaningful and organized approach in which indigenous Bardi Jawi and Nyul Nyul people historically managed, and aspire to continue managing nearby Customary Law-inherited wetlands. The framework presents a meso-scale representation of IKSs that highlights four management principles: custodianship, respectful use, active maintenance, and learning. We describe how affinities for these principles, vis-à-vis other indigenous groups, can also be discerned. Providing a visual framework tool has the potential to assist the application of IKSs to wetland management, and take account of the view that “wetlands need people,” by emphasizing the active, integrated, and reciprocal nature of these knowledge systems in place (associated with traditional lands). That indigenous people value, as well as shape, wetlands, is also considered. By interpreting the framework to support indigenous wetland management (and services to ecosystems) within active cross-cultural work, IKSs promise benefits for people and ecosystems.