Landscape modellers are now capable of combining high resolution spatial data with process models to explore natural resource management scenarios at scales appropriate for decision making, but what of the process of decision making itself? In this chapter we review the applicability of the ‘adaptive management’ paradigm to natural resource management, using regional management of native vegetation by Catchment Management Authorities as an example. We find that progress has been made in the approach to defining management objectives and specifying assumptions behind vegetation change models; however, there remain significant challenges in instituting true management experiments and identifying performance indicators appropriate to support continuous learning. We argue that the ecological and institutional complexity of native vegetation management reinforces the importance of systematic decision protocols. Adaptive management is the most logical approach to decision making where there is uncertainty about the effectiveness of management options, and the opportunity exists to learn and update understanding. This iterative process offers continuous improvements to investment efficiency in native vegetation management.