A ubiquitous problem for community-based regional environmental agencies is to set strategic management priorities among a myriad of issues and multiple stakeholder perspectives. Here, we quantify the strategic management priorities for natural capital and ecosystem services using multicriteria decision analysis (MCDA) in a case study of the South Australian Murray-Darling Basin Natural Resources Management Board (the Board) region. A natural capital and ecosystem services framework was tailored to present decision-makers with a range of potential issues for strategic consideration as goal hierarchies in MCDA. Priorities were elicited from the Board and its four regionally based consultative groups using the Analytical Hierarchy Process and swing weights. Centered log ratio transformed weights were analyzed using multiple pairwise ANOVA comparisons (Dunnett's T3) and hierarchical cluster analysis. Substantial variation in priorities occurred between decisionmakers. Nonetheless, analysis of priorities for assets and services robustly demonstrated that water was the highest priority, followed by land, then biota, with atmosphere the lowest priority. Decisionmakers also considered that environmental management should not impact negatively on built or social capital. Few significant differences in priorities were found between decision-maker groups. However, clusters of manager types were found which represent distinct alternative management strategies, notably the prioritization of either intermediate or final ecosystem services. The results have implications for regional environmental decision-making and suggest that embracing variation in perspectives may be a better way forward for multistakeholder MCDA. The study operationalizes natural capital and ecosystem services by providing strategic priorities for targeting management and policy within the context of communitybased, regional environmental management.