Policy and operational outcomes in biodiversity management are compromised by inconsistent logic and lack of clarity in key terms such as sustainability, environmental quality and resilience. This is due in part to their poor linkage with human values, an essential component of a coherent planning framework. At the same time, the poor definition and classification of planning elements, such as threatening processes, hampers effective use of quantitative decision tools in planning. This paper outlines a framework in which the planning components are linked through cause–effect relationships and driven by human values. When combined with effective classification of planning elements, this framework resolves the issues outlined above and provides a sound basis for planning the management of biodiversity.