Ecosystem-based management (EBM), despite the best efforts of managers, researchers, and policy makers, often falls short of its intended purpose resulting in inadequate protection of resources. Coastal habitats are particularly vulnerable to poor management due to high use and potential for user conflict. EBM can be improved when it is informed by ecological science and considers the socio-economic needs of the community. Communication between scientists and stakeholders can help to prevent adverse outcomes while enhancing protection and sustainability of the coastal environment. In the research presented here, a framework is used to guide and enhance communication between scientists and stakeholders for sustainable management of resources and equity of all users. The outcome of this applied framework is a long-term plan to guide the management of an oyster aquaculture industry using carrying capacity as an estimate for the basis of management decisions. Central to the framework is the Working Group on Aquaculture Regulations (WGAR), which represents a diverse group of stakeholders. The WGAR worked closely with ecological modelers over a two-year period using mass-balance modeling to calculate ecological carrying capacity for oyster aquaculture in two ecosystems: Narragansett Bay and a set of highly flushed temperate lagoons in Rhode Island, USA. Collaboration between scientists and the WGAR greatly improved the models and stakeholder understanding of the science and acceptance of the results. Aquaculture is increasing in coastal regions world-wide and this framework should be easily transferable to other areas suffering from similar user conflict issues.