Coral reef ecosystems are slowly reaching their physical ecosystem boundaries. Urgent action is required by reducing carbon emissions, halt degradation, and initiate restoration and conservation efforts of coral reef ecosystems, and bring coral reefs back to a safe ecosystem operating space. This research study uses a multidisciplinary approach that aims to understand the dynamic behavior of (sub)tropical social-ecological coral reef ecosystems in the Anthropocene and provide insights for future interventions. The study combines literature reviews, expert interviews, cognitive mapping, and system dynamics modeling to determine the variables, relations, and dynamics within coral reef ecosystems, and draw implications for future intervention. The insights are combined in a qualitative and quantitative stock-flow model, through which dynamics of anthropogenic stressors effects on coral reef behavior are examined, and implications for future intervention in social-ecological coral reef ecosystems are drawn. The findings highlight the importance of considering multiple stressors, understanding social-ecological feedbacks, and taking into account as well global as local stressors to restore coral reefs in the face of anthropogenic stressors in the Anthropocene.