Estuarine systems often have degraded ecology and functioning due to the multiple interacting stressors that they face. While conventional management might address such a situation with narrow focus, ecosystem based management provides a more holistic and adaptive option allowing for multiple objectives and values. Such an approach has some commonality with that of the Indigenous Māori of New Zealand, who have holistic, interconnected and intergenerational aspirations. In this study we utilised Te-Rerenga-Parāoa, Whangārei Harbour, Aotearoa New Zealand as a case study to explore how ecological and Māori knowledge systems and approaches may align to address complex multi-stressor and multi-value scenarios common to estuarine systems. To achieve this we co-developed a Bayesian network heuristic modelling tool which provided a probabilistic framework to consider the relationship between stressors and the outcome states for ecological function and cultural values. The process of model development itself was a rewarding exercise of joint learning. For example, this process illustrated that while western ecological values can focus on endpoints such as abundance, cultural values were more diverse, experiential in nature, with value often centred on a cultural practise being enabled, not just the ecological component the value was connected to. Once the model was developed we considered three specific scenarios relating to harbour dredging, environmental degradation from land use changes, and fishery extraction. Model predictions for these scenarios generally matched expectations, but were generic in nature and could therefore benefit from more specificity relating to aspects such as spatial scale and context around cultural interpretation. Overall, the model demonstrated generic utility as an interactive educational tool for resource managers considering the broader impacts (on ecology and cultural values) of major societal challenges.