Western Australia’s Swan River is a complex asset providing environmental, recreational and commercial benefits. Agencies responsible for its management rely extensively on advice from experts, whose preferences may or may not align with those of the community. Using a choice experiment, we compared public and expert preferences for managing the river’s ecology. Modelling revealed heterogeneity in preferences, including within the experts sampled. Ecologists held similar preferences to the minority of public individuals who exhibited the strongest preferences for protecting river ecology. Planners were more similar to the public majority, whose preferences were moderated by the cost of ecological improvement.