The application of the Ecosystem Approach (EA) to the government of aquaculture has been strongly advocated by many scientists and NGOs. However, knowledge gaps exist on actual actor intentions implementing this approach in the European Union (EU) which are often assumed to simply fit with a universalized model. Presenting findings on salmon in Scotland, trout in New Aquitaine (France) and seabass and seabream in Greece, we show that not only do a variety of actor intentions exist, but these can be unexpected. As a result, different forms of 'modernizing', 'competing' and 'appeasing' EU-EAs have been institutionalised. Further, although EA regulation is supported by a well-established EA scientific community, the political project has not followed the scientific one. Consequently, stating that the EA has been applied to aquaculture does not, in and of itself, tell you which socio-ecological interdependencies matter most to actors on the ground, nor how wider debates on the legitimacy of this industry have been addressed.