It is widely accepted that Indigenous ecological knowledge (IEK) is potentially valuable for maintaining biodiversity within linked social-ecological systems, and cultural landscapes in particular. However, IEK is declining globally, along with biodiversity. Adaptive co-management frameworks incorporating both Indigenous and scientific knowledge systems have the capacity for greater success than frameworks embedded within a singular world view. A major challenge exists, however, in identifying pathways for the integration of these knowledge systems. The need to integrate both IEK and science into management is widely recognised; various approaches have been trialled but there are few successful examples. Cooperative research using joint learning is emerging as one potentially useful approach. Here we present an example of applying co-research in a cultural landscape in Australia, the Wet Tropics World Heritage Area, where we aimed to develop linked cultural and biophysical indicators of ecosystem condition. Our approach was founded on five stakeholder-defined core principles for research. The study revealed seven determinants of successful implementation within these principles: strong Indigenous governance; problem-framing and conceptualisation; relationship building; data collection and management; considerations of scale; agreed dissemination of results; and evaluation. We identify cooperative problem-framing as one of the most important determinants, and argue that by starting the co-research process with this task, co-research can assist the equitable convergence of IEK and contemporary natural resource management, thereby potentially enhancing social-ecological system resilience and sustainability.