Adaptive and multi-level governance is often called for in order to improve the management of complex issues such as the provision of natural resources and ecosystem services. In this case study, we analyse the contemporary multi-level governance system that manages water resources and its ecosystem services in a fresh water lake in Sweden. We assess the relative importance and barriers of three commonly highlighted components of adaptive governance: feeding ecological knowledge into the governance system, use of ecological knowledge to continuously adapt the governance system, and self-organisation by flexible institutions acting across multiple levels. Findings reveal that the trickiest aspect of adaptive governance capacity to institutionalise is the iterative nature of feedbacks and learning over time, and that barriers to the spread of knowledge on social-ecological complexity through the governance systems are partly political, partly complexity itself, and partly a more easily resolved lack of coordination. We call for caution in trusting crisis management to build more long-lasting adaptive capacity, and we conclude that a process of institutionalising adaptive capacity is inherently contingent on political process putting issues on the agenda.