Coastal lagoons represent one of the most productive and diverse ecosystems in the United Arab Emirates (UAE) due to their position at the dynamic transition zone between land and sea. UAE’s coastal lagoons, also known as khors, are home to a diverse assemblage of organisms, including many resident and endangered species that rely on the interconnected mosaics of habitat types (mangroves, seagrass, saltmarshes, mudflats) that also provide a wealth of benefits to society. These ecosystem characteristics, and the need to ensure their sustainable development, have made lagoons a high priority for conservation in the Emirates. Primarily located along the UAE’s Arabian Gulf coast, coastal lagoons have been highly impacted by urbanization that modifies or removes habitats and disturbs wildlife due to increased pollution from artificial light, noise and chemicals. Coastal lagoons in the UAE are in urgent need of protection to ensure that current and future generations continue to enjoy healthy coastal ecosystems. Integrated ecosystem-based management that is supported by local institutions and includes participatory monitoring through citizen science programmes will increase public engagement and advance progress towards the goal of living in harmony with nature.