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Environmental management strategies aim to protect or repair ecological assets (ecosystems, species) so that their ecological and social values can be preserved. However, creating an effective strategy is difficult because multiple government departments are involved and because water and land use legislation and policy instruments are often fragmented. A key obstacle that is often overlooked is the spatial mismatch between ecological processes and institutional organisation (i.e., legislative framework and government departments). Successful management depends on the ability to cultivate resilient ecosystems through institutional reforms that take into account the complexity of ecosystems while supporting cross-sectoral and scale-dependent decision-making within the science–policy interface. Here, we use a case study approach to illustrate how collective strategic decisions can be made to manage a valued ecosystem situated within an urban matrix. We used a three-step framework to guide our approach and commenced by identifying a range of adaptation measures (i.e., management interventions) and the actors responsible. For each adaptation measure, we then investigated (i) mismatches among ecosystem and institution scales and levels; (ii) institutional barriers; and (iii) the role of actors in decision making. We use this information to identify ‘decision pathways’: i.e., a flexible decision-making platform that assists stakeholders to make strategic short- and long-term decisions. Key insights included the discussion of policy and practical experiences for ecosystem management at different levels and the necessary conditions to …