<p>Indonesia has experienced significant mangrove loss due to aquaculture expansion, particularly for shrimp farming, leading to the degradation of habitats and critical ecosystem services such as carbon storage, coastal protection, and fish spawning grounds. Ecosystem based aquaculture approaches offer a pathway to both mitigate environmental impacts and support sustainable seafood production. Here we explore the implementation of the Shrimp-Carbon Aquaculture (SECURE) approach in Berau Regency, East Kalimantan, Indonesia, which integrates mangrove restoration with organic shrimp farming to achieve sustainable aquaculture. Using environmental DNA (eDNA) metabarcoding to detect species from DNA shed into the environment, we assessed impacts of SECURE intervention compared to traditional ponds and found increased abundance of key taxonomic groups associated with healthy aquatic ecosystems, such as phytoplankton Chaetoceros, Chlorophyceae, and Cryptomonadales and zooplankton Calanoida and Cyclopoida. We then conducted a spatial prioritisation analysis to identify additional areas for SECURE implementation, considering mangrove restoration and protection potential, profitability, and intervention costs. High-priority ponds for restoration were typically set back from riverbanks, large, and spatially clustered, indicating opportunities for cost-effective, strategic expansion. This study underscores how spatial prioritisation can support strategic implementation of aquaculture to balance ecosystem-based aquaculture development with environmental conservation, offering a replicable framework for other regions facing similar challenges. This approach provides a pathway for achieving long-term sustainability in aquaculture, contributing to global food security and ecological resilience.</p>