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Success or failure of a polycentric system is a function of complex political and social processes, such as coordination between actors and venues to solve specialized policy problems. Yet there is currently no accepted method for isolating distinct processes of coordination, nor to understand how their variance affects polycentric governance performance. We develop and test a building-blocks approach that uses different patterns or “motifs” for measuring and comparing coordination longitudinally on Australia's Great Barrier Reef. Our approach confirms that polycentric governance comprises an evolving substrate of interdependent venues and actors over time. However, while issue specialization and actor participation can be improved through the mobilization of venues, such a strategy can also fragment overall polycentric capacity to resolve conflict and adapt to new problems. A building-blocks approach advances understanding and practice of polycentric governance by enabling sharper diagnosis of internal dynamics in complex environmental governance systems.