Abstract Estimating the value of entire ecosystems in monetary units is difficult because they are complex systems composed of non-linear, interdependent components and the value of the services they produce are interdependent and overlapping. Using the Great Barrier Reef (GBR) as a case study, this paper explores a new ‘whole ecosystem’ approach to assessing both the importance (to overall quality of life) and the monetary value of various community-defined benefits, some of which align with various ecosystem services. We find that provisioning services are considered, by residents, to be less important to their overall quality of life than other ecosystem services. But our analysis suggests that many community-defined benefits are overlapping. Using statistical techniques to identify and control for these overlapping benefits, we estimate that the collective monetary value of a broad range of services provided by the GBR is likely to be between $15 billion and $20 billion AUS per annum. We acknowledge the limitations of our methods and estimates but show how they highlight the importance of the problem, and open up promising avenues for further research. With further refinement and development, radically different ‘whole ecosystem’ valuation approaches like these may eventually become viable alternatives to the more common additive approaches.