This article concentrates on five marine sectors active in the marine environment (fisheries, offshore renewable energy, offshore oil and gas, navigation, and coastal tourism) and on non-industry stakeholders represented by environmental Non-Governmental Organizations (eNGOs) and how they have engaged in the Marine Strategy Framework Directive (MSFD) stakeholder consultation process and what they foresee as potential challenges for implementation. The social, economic, and political significance of the five sectors and eNGOs in relation to the MSFD is presented, as well as a description of the stakeholder consultation process as experienced by representatives from the sectors and eNGOs, in addition to an illustration of the EU policy landscape associated with the sectors. Three central themes emerge in relation to implementing the MSFD and the ecosystem-based approach to management in EU marine waters: (a) Boundaries; (b) policy and management coordination; and (c) balancing values and user conflicts have been explored. The paper concludes that from a governance perspective it is clear that the MSFD has not been that well-thought through. The consistency of the overall legal frameworks and specific regulations related to marine management have created legal vagueness and subsequently caused legal uncertainties leading to conflicting policies and regulations having unclear boundaries. Furthermore, it has been demonstrated the dilemmas facing various sectors related to MSFD implementation and shown how unequally prepared different sectors are to participate in this policy.