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Conflicting priorities and lack of integrated management planning is a key obstacle for resolving the current state of affairs. An ecosystem-based approach to management, based on transnational spatial planning, would be a strong tool to overcome this challenge. Spatial planning, which integrates complex information on marine landscapes, habitat distribution, economic values and conservation status with information on user practices and stakeholders dependence on natural resources, is a needed for a holistic planning and informed decision-making. It would also contribute to a cost-effective and successful implementation of EC Directives, HELCOM recommendations and related policy documents. For example, transnational spatial planning can assist implementation of the measures set in place for protecting the ecosystem structure, such as the Natura 2000 Network, by facilitating a balanced designation of sites representing a continuum of marine habitats and promote "blue corridors" between protected sites.