The coastline of Qatar is a rich mosaic of productive and diverse ecosystems including mangrove forests, intertidal mudflats (sabkha), seagrass beds, and coral reefs. These ecologically interconnected ecosystems contain a substantial proportion of Qatar’s total biodiversity, and support an estimated 97% of the >US$ 67 million in annual commercial fisheries, the highest value resource sector after petroleum. The extreme environmental conditions that characterize Qatar has led to fauna that are robust compared with other regions, but makes them highly sensitive to further pressure from anthropogenic stress. These vulnerable ecosystems have come under increasing pressure in recent decades as a result of dramatic expansion of coastal development, and threats to these ecosystems are likely to accelerate in the coming years as Qatar’s economy and population continue to grow. Although environmental regulation had historically lagged behind the rapid pace of development, in recent years Qatar’s leadership has aggressively expanded environmental management as a result of the growing awareness of the importance of coastal ecosystems. While these improvements are encouraging, management remains challenged by its current sectorial, project-driven focus. Ecosystem-based management (EBM) offers an opportunity to overcome these challenges by integrating impacts from across all major activities in multiple sectors and considering their cumulative effects on ecosystem services and products. While an EBM approach would require modest reprioritizing of existing processes and attention to addressing deficiencies in data needed to support decision making, it has the potential to greatly enhance the efficiency and effectiveness of coastal zone management. The article closes by summarizing a recently initiated research project on coral reefs and seagrass beds in Qatar which can serve as a model for development of the EBM approach for other coastal ecosystems in Qatar.