Freshwater resource management is becoming increasingly complex as human pressure increases on available water resources, and as more participatory transparent decision-making frameworks are being advocated within water management. Complexity is further increased when environmental flow programs are integrated into existing water management programs. Adaptive management frameworks present an obvious choice for integration and implementation of environmental flows, but have so far failed to become the dominant framework. The research presented here highlights the ability of a strategic adaptive management (SAM) approach within an environmental flow program in the Murray Darling Basin of Australia to facilitate planning and implementation of environmental flows. The SAM approach did show that adaptive management can deal with the complexities of designing and implementing environmental flows within complex social-ecological systems, but can have limitations in the long-term. The approach highlighted the importance of social processes within adaptive management, emphasizing that a focus on inclusiveness, commitment, and transparency aimed at building understanding, trust, and ownership are key processes for implementation. In this specific case study, successful implementation was achieved through structured co-design of initial programs and participatory decision-making throughout. However, the SAM approach also showed that adaptive management is vulnerable to challenges in the long-term when resources and expertize change.