Expansion of a development area can negatively impact ecosystems by decreasing or fragmenting habitats. With increased awareness of the importance of biodiversity and ecosystem services (BES), ecosystem service evaluations have attracted increased attention. The geography surrounding the city of Incheon is ecologically valuable because of its ecological diversity, attributed to its mudflats and coastal terrain. This study analyzed changes caused by the Incheon Free Economic Zone (IFEZ) agreement in the ecosystem services of this area using uses the Integrated Valuation of Ecosystem Services and Tradeoffs model and assesses the impacts of BES before and after the implementation of the agreement. Results revealed that carbon fixation and habitat quality decreased by approximately 40% and 37%, respectively, owing to the development caused by the agreement (p < 0.01). Additionally, endangered species and migratory birds were not protected by the terms of the IFEZ, and a decline in habitats, prey, and breeding sites was observed. This study suggests that the value of ecosystem services and the expansion of conservation areas should be considered part of ecological research under economic free trade agreements.