There has long been a tension between environmental regulation and the European Common Fisheries Policy (CFP), which has been addressed over time through progressive reform of the CFP. It is now recognised that Member States may comply with their obligations under EU nature conservation law by taking unilateral non-discriminatory measures within their territorial seas to protect the marine environment from threats posed by fishing. Nevertheless, fundamental uncertainties remain when it comes to the application of these obligations to offshore waters. This article explores the options available to coastal states in this context and the weaknesses of the procedures introduced to the reformed CFP in 2013. It is argued that compliance with nature conservation law in the context of fisheries is not discretionary and that in the absence of measures agreed at the EU level, Member States must comply with their obligations under the Habitats Directive in their capacity as a flag state. Finally, the article addresses the implications of Brexit for the protection of European Marine Sites in UK waters, suggesting that Brexit offers opportunities to strengthen the protection of marine ecosystems by making future access arrangements for foreign fishing vessels conditional upon compliance with nature conservation laws.