This paper presents an approach for preparing a comprehensive national marine ecosystem assessment and its application to the marine and coastal areas of the State of Kuwait. The approach is based on a set of principles to enable diverse data sources, of differing data quality and salience, to be combined into a single coordinated national assessment of marine ecosystem status to support the implementation of ecosystem-based management. The approach enables state assessments for multiple components of the marine ecosystem to be undertaken in a coordinated manner, using differing methods varying from quantitative to qualitative assessments depending on data and indicator availability. The marine ecosystem assessment is structured according to 6 major themes: i) Biodiversity, ii) Commercial Fisheries, iii) Food and Water Quality for Human Health, iv) Environmental Pollution, v) Eutrophication and Harmful Algal Blooms, and vi) Coastal Process and Oceanography. Comprehensive ecosystem assessments are an essential part of implementing the ecosystem approach, however detailed data directly related to clear, specified numerical management targets covering all aspects of a marine ecosystem are rarely available. The development of a State of the Marine Environment Report (SOMER) for Kuwait demonstrate that a coordinated comprehensive ecosystem assessment can be conducted using disparate data, and in relation to partially specified regulatory management objectives. The Kuwait SOMER highlighted the issues of coastal pollution, particularly sewage for human health and the environment. It shows that the rapid urbanization of Kuwait has led to significant changes in the ecology, with clear impacts on coral reef health, the availability of nesting locations for turtles and habitats for migratory birds. Long-term changes in nutrient input, via waste water and modified freshwater inputs is resulting in demonstrable impacts on a range of marine species and habitats within Kuwait marine waters. It also supports the move towards a regional approach required due to transboundary properties of many of the ecosystem components, drivers and pressures.