Conservation zoning is a planning process that has been used within protected areas to spatially establish and communicate conservation goals and reduce user conflicts. Here, we explored a resilience-based approach to zoning in Fathom Five National Marine Park, Lake Huron, Canada, using the decision support tool Marxan with Zones, a command line program that we interfaced with our Geographic Information System (GIS). Conservation features were identified and organized into general themes of ecosystem structure, ecosystem function, and social structure. Target values for these features were set to achieve representativeness, replication, and connectivity goals, while minimizing social, political, and economic costs. Although 100 different near-optimal solutions were generated, we paid particular attention to the “best” and “summed” solutions. Implementation recommendations also included considerations for active learning, adaptive management, and good governance. The tools and methods provide an example for managers of other protected areas interested in maintaining and building ecosystem resilience..