Social acceptability has become an important issue, influencing public and private decision making in many different areas of society, including the management of uses of common marine resources and space. As these uses intensify and social interactions become more complex, effective governance is a prerequisite for sustainable decision making. Participatory approaches are broadly recognised as a tool for involving stakeholders in the decision-making process to increase the acceptability of collective choices. However, despite the recommendations of new governance frameworks which promote inclusive and democratic bottom-up approaches, there is an increased complexity to apply such approach at local level. This paper aims to capture this complexity through the analysis of the local agency-led participative process and ad-hoc interviews with coastal users to understand whether and how perception and attitudes towards aquaculture evolve throughout the process. Here we present the result of a 3-year collaborative action science-policy with the agency responsible to manage aquaculture in Andalucía region (South of Spain). Even though the effectiveness of this participatory process in aquaculture planning should be assessed over the long-term, here we have identified a number of social, environmental and economic elements that can generate local opposition, especially by traditional fishers. The paper highlights the fact that the inclusion of stakeholders in the decision-making processes is not sufficient ensure the acceptance of aquaculture development. The effectiveness of the participatory processes is limited by the lack of institutional frameworks to accompany these processes, by the insufficient skills and expertise in engineering participation of the Administration staff and the poor integrated vision in policy making. As a result, the lack of coherence between political objectives constructed on a national or European scale and the complex social reality of the territory scale can lead to social opposition as experimented by the aquaculture sector.