Population persistence in the marine environment is driven by patterns of ocean circulation, larval dispersal, ecological interactions, and demographic rates. For habitat‐forming organisms in particular, understanding the relationship between larval connectivity and meta‐population dynamics aids in planning for marine spatial management. Here, we estimate networks of connectivity between fringing coral reefs in the northwest shelf of Australia by combining a particle tracking model based on shelf circulation with models of subpopulation dynamics of individual reefs. Coral cover data were used as a proxy for overall habitat quality, which can change as a result of natural processes, human‐driven impacts, and management initiatives. We obtain three major results of conservation significance. First, the dynamics of the ecological network result from the interplay between network connectivity and ecological processes on individual reefs. The maximum coral cover a zone can sustain imposes a significant nonlinearity on the role an individual reef plays within the dynamics of the network, and thus on the impact of conservation interventions on specific reefs. Second, the role of an individual reef within these network dynamics changes considerably depending on the overall state of the system: a reef's role in sustaining the system's state can be different from the same reef's role in helping the system recover following major disturbance. Third, patterns of network connectivity change significantly as a function of yearly shelf circulation trends, and nonlinearity in network dynamics make mean connectivity a poor representation of yearly variations. From a management perspective, the priority list of reefs that are targets for management interventions depends crucially on what type of stressors (system‐wide vs. localized) need addressing. This choice also depends not only on the ultimate purpose of management, but also on future oceanographic, climate change, and development scenarios that will determine the network connectivity and habitat quality.