Adaptive management has been promoted as a structured approach to learning in response to the uncertainty associated with managing complex systems. We developed and tested a protocol to guide an adaptive approach to water quality management in north-eastern Australia. The protocol articulates a framework for documenting uncertainties and performance expectations, negotiating feedback and anticipating iterative and transformative responses to future scenarios. A Water Quality Improvement Plan developed for the Tully–Murray catchment in the Great Barrier Reef region was used to test the protocol and three benefits of its use were identified. First, developing rigorous and timely monitoring and evaluation ensures that opportunities for iterative planning are realised. Second, anticipating future endogenous or exogenous changes to the plan enables the early initiation of actions to inform transformative planning responses. Finally, the protocol exposed the need to coordinate multi-scalar responses to tackle environmental knowledge and management uncertainties and assumptions. The protocol seeks to provide a practical translation of adaptive planning theory that will enable the benefits of adaptive management to be realised on the ground.