Blue carbon ecosystems (BCEs), including salt marshes and seagrass beds, are vital for climate change mitigation, sequestering carbon at rates much higher than terrestrial ecosystems. Despite their significance, BCEs are increasingly threatened by both natural and human-induced pressures. This study aimed to advance understanding of blue carbon in the EU, focusing on greenhouse gas (GHG) reporting, wetland mapping, and sequestration knowledge. Findings highlight inconsistencies in wetland classification and GHG reporting, between EU countries, especially for coastal wetlands. The research reveals gaps in conservation, with many BCEs lacking adequate protection and management. Through improved mapping and monitoring, the study proposes enhanced policy recommendations for better conservation and integration of BCEs into EU climate strategies. Furthermore, the study investigates blue carbon restoration projects, emphasizing barriers such as the absence of reliable sequestration metrics and uncertain financial models. The results stress the importance of standardizing reporting, improving restoration efforts, and leveraging diverse funding mechanisms to maximize the climate mitigation potential of BCEs.