On-ground natural resource management actions such as revegetation and remnant vegetation management can simultaneously affect multiple objectives including land, water and biodiversity resources. Hence, planning for the sustainable management of natural resources requires consideration of these multiple objectives. However, planning the location of management actions in the landscape often treats these objectives individually to reduce the process and spatial complexity inherent in human-modified and natural landscapes. This can be inefficient and potentially counterproductive given the linkages and trade-offs involved. We develop and apply a systematic regional planning approach to identify geographic priorities for on-ground natural resource management actions that most cost-effectively meet multiple natural resource management objectives. Our systematic regional planning approach utilises integer programming within a structured multi-criteria decision analysis framework. Intelligent siting can capitalise on the multiple benefits of on-ground actions and achieve natural resource management objectives more efficiently. The focus of this study is the human-modified landscape of the River Murray, South Australia. However, the methodology and analyses presented here can be adapted to other regions requiring more efficient and integrated planning for the management of natural resources.