Marine aquaculture of bivalve molluscs is an important economic activity in Santa Catarina State, Brazil, with more than 5000 persons directly and indirectly involved and an annual revenue of US$ 18 million in 2013. In the first decade of this activity, a lack of proper regulation imposed multiple obstacles to the sustainable management of local shellfish farming. The occupation of marine space occurred in a disorderly manner, and the unplanned development led to unfavourable conditions that threatened the sustainability of the industry. This study describes how better planning and management tools have improved governance of marine aquaculture in Santa Catarina State. The process included development of a legal framework for aquaculture planning, elaboration of local development plans with a participatory and multidisciplinary approach, development of a geographic information system to identify favourable areas and creation of a Webbased aquaculture management system. The combined application of these actions, along with continuing extension services, is expected to contribute to the regulation of 837 shellfish farming areas, the expansion of farming activity, the mitigation of the environmental and visual impacts caused by coastal aquaculture and an increase in the public health of shellfish consumers. In this manuscript, we report an example of how the application of better planning and management of the aquaculture sector can prepare the industry for a sustainable growing cycle.