Coastal lagoons are ecosystems with great environmental and socioeconomic value. However, these natural systems are especially vulnerable to climatic and anthropogenic pressures, such as intensive agriculture and extensive urbanization as a consequence of the tourist development. Despite the vulnerability and complexity of these ecosystems, there has been limited development of novel techniques which can provide real-time monitoring, analysis and management of these critical resources. Beyond being useful for policy-making procedures at multiple levels of granularity, these tools can increase local and citizen awareness of environmental impacts. SMARTLAGOON project intends to develop a digital twin to build a systemic understanding of the socio-environmental inter-relationships affecting costal lagoons and their ecosystem. It will digitally replicate the policy-making procedure of these complex socio-environmental systems by combining, analyzing and interpreting data from different sources; including efficient in-situ IoT infrastructures with edge computing capabilities that reduce the overall system’s carbon footprint, remote sensing technologies, social media sensing, open-data repositories and data from human behavior, economics and the social sciences, by making recourse to advanced AI, NLP, physically-based and citizen science models. As a case study, SMARTLAGOON focuses on the Europe’s largest salt water coastal lagoon, i.e., Mar Menor (Murcia, Spain), which has suffered serious environmental degradation due to several socio/environmental reasons. We will jointly develop our tool with citizens, stakeholders and policy-makers of this area to address their needs and requirements, following an agile methodology to ensure practical and useful results for this particular scenario in the first instance and extend to other coastal lagoons in the second instance.