The United Nations Sustainable Development Goals (SDGs) and their corresponding targets are significantly interconnected, with many interactions, synergies, and trade-offs between individual goals across multiple temporal and spatial scales. This paper proposes a framework for the Integrated Assessment Modelling (IAM) of a complex deltaic socio-ecological system in order to analyze such SDG interactions. We focused on the Sundarban Biosphere Reserve (SBR), India, within the Ganges-Brahmaputra-Meghna Delta. It is densely populated with 4.4 million people (2011), high levels of poverty, and a strong dependence on rural livelihoods. It is adjacent to the growing megacity of Kolkata. The area also includes the Indian portion of the world’s largest mangrove forest––the Sundarbans––hosting the iconic Bengal Tiger. Like all deltaic systems, this area is subject to multiple drivers of environmental change operating across scales. The IAM framework is designed to investigate socio-environmental change under a range of explorative and/or normative scenarios and explore associated policy impacts, considering a broad range of subthematic SDG indicators. The following elements were explicitly considered: (1) agriculture; (2) aquaculture; (3) mangroves; (4) fisheries; and (5) multidimensional poverty. Key questions that can be addressed include the implications of changing monsoon patterns, trade-offs between agriculture and aquaculture, or the future of the Sundarbans’ mangroves under sea-level rise and different management strategies. The novel, high-resolution analysis of SDG interactions allowed by the IAM will provide stakeholders and policy makers the opportunity to prioritize and explore the SDG targets that are most relevant to the SBR and provide a foundation for further integrated analysis.