Benthic animals which live on the marine sediment play an important role in the basis of marine food web and highly sensitive indicator for environmental assessment. Meanwhile, eutrophication has been considered as one of the most important environmental problems in coastal areas worldwide. However, high organic matter inputs, as a secondary effect of eutrophication, increase the availability of food for benthic animals. Studies and academic literatures focusing on benthic communities structure and function in the tropical coastal water of Indonesia is limited. In this book the relationship between gradients of organic enrichment and the community structure, function, clearance rates of the benthic animals and its carrying capacity are discussed. The benthic ecological concepts e.g. Pearson – Rosenberg model, diversity indices, and ecological groups indicator (AMBI) are tested it’s suitability for the tropical region. Finally, a framework of benthic – pelagic coupling on the coastal water is illustrated. This book is suitable for students and researchers, professional consultants in marine ecology, fisheries and environmental sciences as well as managers for coastal management.