Indonesian coastal cities grow significantly with the strategic economic value. Jakarta is no exception. As the capital city and metropolitan, with the complexity of social and environmental long-term issues, the rapid growth of city economy and development of Jakarta coastal area and generates the big impact on social and environment. The marine pollution in Jakarta Northern Coast area causes the environmental and social issues in the informal fishermen settlement. The local communities were forced to adapt with these challenges, as there was limited affordable living environment alternative available for the poor. Government has planned the long-term agenda to mitigate the risks and the better future for the local community and environment. There was gap between the ground challenges faced by the fishermen community and the government related policies in achieving the better coastal development. This study presents a case-based analysis in Jakarta Northern Coast Fishermen Settlement. Results show that the multilayer backgrounds of social, economy and governance roles are complex interrelated factors to overcome the long term social and environmental challenges. A holistic approach is suggested for a strategic solution for a more sustainable and resilient Jakarta Northern Coast Area. © 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.