The merits of polycentric climate governance have attracted considerable discussion. On the one hand, polycentric governance offers an alternative to top-down state-centric forms that have so far proven elusive. On the other, highly networked systems increase coordination challenges. Less attention has been paid to the varying capacities required to achieve coordination. In this article we explore the coordination of polycentric governance via a case study of sargassum influx management in the Caribbean. Since 2011, large quantities of sargassum seaweed have been washing up on Caribbean beaches with adverse socio-economic impacts. Our analysis of sargassum management policies reveals that a nascent polycentric system has generated significant cooperation in policy development and application across the region. However, there remain national capacity deficits to engage in this form of governance and to implement agreed actions. We conclude that advocates of a polycentric climate governance regime need to consider how capacity shapes participation, to the advantage of the largest and strongest. Polycentric governance can be useful for solving disparate cross-border environmental problems, but it also imposes a cost on the smallest that has thus far been unacknowledged and undertheorized.