Representing 9% of the land worldwide, the coastal zone is a highly populated part of the land, where economic and social growth continuously arise. An expected consequence of rapid development on the coastal zone is the creation of significant environmental pressures connected to human activities. Within this framework, the need to use the ecosystem services concept under the prism of sustainable development has risen to increase the provision of services to the people through an ecosystem approach using the human–environment interaction. The aim of this paper is to form an integrated approach for sustainable blue economy in a coastal ecosystem, using the SDGs and the ecosystem services frameworks and exploring the interlinkages of the ecosystem’s parameters from both sides. The outcome of this study is the formation of a decision-making tool for sustainable blue economy in a coastal ecosystem, which classifies the SDGs with a specific factor, according to their importance for the sustainable blue economy, and helps stakeholders prioritize their actions toward the achievement of sustainability in the specific ecosystem. A case study of this approach is Elefsis Gulf, a coastal ecosystem in the eastern Mediterranean, located 18 km from the historic city of Athens, Greece.