Natural resource management agencies need to incorporate community values into regional planning. In this paper we use the concept of natural capital and ecosystem services to map community values towards the environment at the landscape level. Interviews and values mapping was undertaken with 56 natural resource management decision-makers and community representatives in the South Australian Murray-Darling Basin region. The spatial distribution of values and threats for natural capital and ecosystem services was quantified. Indicators were assembled to quantify value richness, diversity, rarity, and risk and these are used to refine systematic regional planning for natural resource management. Hotspots were identified for biophysical management and community value. Smart spatial targeting of natural resource management can be used to address biophysical objectives and maximise social values.