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Whale watching is a billion dollar industry worldwide. One of the most popular species for whale watching is the humpback whale (Megaptera novaeangliae). The migratory corridors, feeding, resting and calving sites which are used for whale watching may be influenced by changing ocean currents and water temperatures. Here, we used an innovative approach addressing the emerging issue of climate change on the whale watch industry. This involved participatory modelling using key stakeholders for the whale watching industry to develop a systems conceptualisation model for evaluating the potential effects of climate change based on a case study from the east coast of Australia. This participatory approach allowed us to identify the causal linkages (including feedback pathways) between different “Elements” of the system within which the whale watching industry operates. It also allowed us to integrate multiple drivers covering socio-economic and environmental aspects including climate change (e.g. temperature), policy (e.g. number of boats), ecology (e.g. number of whales) and socio-economics (e.g. number of tourists) to evaluate the changes in the overall system. We then developed a Bayesian belief network model from the systems conceptualisation on which stakeholders identified a priority issue (Profitability). Stakeholders provided the structure and the quantification of this model, and a sensitivity analysis was carried out to help identify important intervention points for the industry. Overall, our research illustrates how such a modelling process can assist local tourism operators and authorities in making rational management decisions within a holistic or systems-based framework and its approach is applicable to other regions.