Anthropogenic pressure on freshwater ecosystems is increasing, and often leading to unacceptable social-ecological outcomes. This is even more prevalent in intermittent river systems where many are already heavily modified, or human encroachment is increasing. Although adaptive management approaches have the potential to aid in providing the framework to consider the complexities of intermittent river systems and improve utility within the management of these systems, success has been variable. This paper looks at the application of an adaptive management pilot project within an environmental flows program in an intermittent stream (Tuppal Creek) in the Murray Darling Basin, Australia. The program focused on stakeholder involvement, participatory decision-making, and simple monitoring as the basis of an adaptive management approach. The approach found that by building trust and ownership through concentrating on inclusiveness and transparency, partnerships between government agencies and landholders were developed. This facilitated a willingness to accept greater risks and unintended consequences allowing implementation to occur.