In the last 20 years, the EU has adopted some rather ambitious pieces of legislation with the aim to achieve a good environmental status in freshwater and marine ecosystems. Both the Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD) have a strong focus on the natural environment and biological criteria for assessing the status of the relevant ecosystems. In the same time period, much research on environmental governance has focused on the interconnectedness of social systems and ecosystems, so-called social-ecological systems (SES). While having high aspirations, the legal frameworks underpinning current EU water and marine management do not necessarily reflect the advances of contemporary science relating to SES. Using the geographical intersection of the two directives, i.e., coastal waters as a focal point, the paper explores the inchoate integration of social and ecological perspectives in the EU marine governance. What are the main challenges for the current EU legal regimes for managing coastal waters in a way that builds on the understanding of social and ecological systems as interconnected? Having explored the two directives, the paper introduces the possibility of using marine spatial planning (MSP), and the EU directive establishing a framework for maritime spatial planning (MSPD) as a bridge between the social and ecological dimensions and discusses what implications this would have for the current system for governing coastal waters in Europe.