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Transboundary conservation has an important, yet often undervalued, role in the international conservation regime. When applied to the legally ambiguous and interconnected marine environment this is magnified. The lack of clear guidance for transboundary marine conservation from the international conservation community exacerbates this problem, leaving individual initiatives to develop their own governance arrangements. Yet, well-managed transboundary marine protected areas (MPAs) have the potential to contribute significantly to global conservation aims. Conversely, in a period where there is increasing interest in marine resources and space from all sectors, the designation of MPAs can create or amplify a regional conflict. In some instances, states have used MPAs to extend rights over disputed marine resources, restrict the freedom of others and establish sovereignty over maritime space. Six case studies were taken from Europe, North Africa and the Middle East to illustrate how states have interpreted and utilized different legislative mechanisms to either come together or diverge over the governance of marine resources or maritime space. Each of the case studies illustrates how different actors have used the same legislative tools, but with different interpretations and applications, to justify their claims. It is clear that the role of science combined with a deeper engagement with stakeholders can play a critical role in tempering conflict between states. Where states are willing to cooperate, the absence of clear guidelines at the global level means that often ad hoc measures are put into place, with the international frameworks then playing catch up. Balancing different jurisdictional claims with the conservation of the marine environment, whilst considering the increasing special economic interests will become increasingly difficult. Developing a transboundary conservation tool, such as the simple conservation caveats found in the Barcelona Convention and Antarctic Convention, which allow for the establishment of intergovernmental cooperation without prejudicing any outstanding jurisdictional issue, would provide a framework for the development of individual transboundary MPAs.

As a response to increasing human pressures on marine ecosystems, the legislation aimed at improving the conservation and management of marine coastal areas in European and Contiguous Seas (ECS) underwent crucial advances. ECS, however, still remain largely affected by increasing threats leading to biodiversity loss. Here, by using emblematic case studies and expert knowledge, we review current conservation tools, comparing their application in different areas to assess their effectiveness, potential for synergies, and contradictions. Despite regional differences in their application, the existing legislative frameworks have the potential to regulate human activities and to protect marine biodiversity. However, four challenges remain to be addressed to fully achieve environmental policy goals: (1) Lack of shared vision representing a limitation in transboundary collaboration. Although all EU countries are committed to fulfil EU Directives and other binding international legislative acts, a remarkable heterogeneity exists among countries in the compliance with the common legislation on conservation and in their degree of implementation. (2) Lack of systematic procedures for the selection of protected marine sites. Regional and national approaches in designating Natura 2000 sites and nationally designated marine protected areas (MPAs) reflect varying conservation targets and importance of conservation issues in political agendas. (3) Lack of coherent ecological networks. Natura 2000 sites and other MPAs are still far from reaching the status of effective networks in all considered case studies. (4) Hotspot of conflicts with private economic interests prevailing over conservation aims. Recommendations are given to overcome the fragmented approach still characterizing the conservation and management of coastal marine environments. Holistic, integrated, ecosystem-based, cross-cutting approaches can avoid conflicts among institutions so as to provide effective and timely solutions to current and future challenges concerning the conservation and management of marine ecosystems and associated goods and services.