Mar Piccolo in Taranto is a coastal basin that is heavily exploited for commercial mussel farming, producing an annual income of ~EUR 13 million. The longstanding renown of the Taranto mussels has suffered over the last decade following policy decisions to relocate a portion of the urban sewage to an outfall outside of Mar Piccolo and to expand the mussel farms. The resulting decline in mussel quality and the quandary of how to restore stability to Taranto mussel production became the focal issue for our application of the Systems Approach Framework. We simulated the ecological, economic, and social interactions that affect the Mar Piccolo coastal system with a particular focus on mussel production. Stakeholders and mussel farmers contributed to the model implementation by participating in meetings during the entire exercise. Our simulation analysis provided for them a means for understanding of the effects of alternative policy scenarios on the system. We present here the results that demonstrate the value of the systems approach concerning: 1) an operational ecosystem model; 2) sustainable strategies for the management of mussel culture; 3) improved methods for communicating with stakeholders, policy, and the public. These results have already positively influenced how the Mar Piccolo is studied, managed, and perceived.