Sechura Bay, Peru is a highly productive marine resource system, but rapid institutional changes and increasing climate impacts make the future uncertain for local livelihoods dependent on the bay. In the last two decades following the introduction of high-value scallop mariculture for export to international markets, the previous largely informal and open-access system in the bay has transformed towards formalization. What has emerged is a complex arrangement of formal institutional structures dominated by large processing firms and private property regimes, yet still characterized by many informal arrangements and activities, and simultaneously facing a high degree of uncertainty from warming ocean temperatures, harmful algal blooms, and other climate impacts. In this study, we apply participatory modeling, specifically fuzzy cognitive mapping, through a series of iterative workshop activities to model this complex social-ecological system from the perspective of local people. These people are embedded in various marine resource subsectors which are often competing, conflicting, coexisting, and codependent on each other. We synthesize and reflect on benefits and limitations of participatory modeling for (1) navigating conflict and consensus-making in marine resource governance, by exploring similarities and differences between mental models, social group identity, and normative values, and for (2) navigating uncertainty in marine resource governance, by using mental models and “what-if?” simulations to inform discussion and deliberation with local people regarding viable policy and adaptation strategies under potential future governance and environmental actors scenarios.