This article contributes to our understanding of transboundary environmental management regimes through the application of an analytical framework that facilitates an exploration of the co-existence of conflict and cooperation. Rather than framing conflict and cooperation as mutually exclusive states at opposite ends of a spectrum, we seek to understand the ways in which cooperation can exist at the same time as conflict. We apply this framework to a study of conservation management in a transboundary area at the intersection of the Democratic Republic of Congo, Rwanda and Uganda. We identify two actual and one hypothetical phase of conflict–cooperation relations, in a landscape notorious for some of the worst violence of the last two decades. We map the evolution of phases of transboundary protected area management against the evolving security context, and we find that this approach has greater explanatory power than previous approaches that polarize conflict and cooperation. In particular, it helps us to understand the drivers of environmental cooperation, including the evolving characteristics of that cooperation. This new way of understanding the relationship between environmental management and security also enables us to reconsider the potential for environmental management to be instrumental in working towards interstate security objectives, for example through peace parks. We don’t find that the ‘low politics’ of environmental management should be seen as a predictable and manageable determinant of international relations. But an understanding of the coexistence of conflict and cooperation does also point to a more complex, non-linear relationship between low and high politics.