The clam fishing and aquaculture system in the Venice Lagoon still appears insufficiently resilient to buffer external and internal perturbations, such as productivity fluctuations, unregulated fishing, and market related dynamics, despite the efforts of regional and local authorities to achieve the sustainable development. According to the System Approach Framework (SAF), based on previous studies and stakeholder interactions, we developed a model integrating ecological, social, and economic (ESE) aspects. We chose the aspects necessary to represent the essential dynamics of major ecological, social, and economic clam farming system components to project the consequences of implementing alternative management policies and to address the ecological and social carrying capacity. Results of the simulations suggest that a properly managed farming system can sustain an acceptable income and support the local community, while reducing negative environmental impacts, social conflicts, and consumer health risks and improving system resilience. The results highlight the importance of an interdisciplinary, participatory, and adaptive approach in planning the management of this important renewable resource.