Assessing the quality of coastal waters is a vital issue for society and managers. Performing a holistic assessment, which incorporates not only physico-chemical but also biological and ecological notions, is a major challenge for scientists. Consequently, the design and implementation of biomonitoring tools has become a major field in applied ecology, resulting in an exacerbate market of biotic indices. In this book, we revise the offer of this market in the field of coastal waters, and evaluate the strengths and weaknesses of the available tools from the point of view of the users'' needs. Additionally, we show several examples of monitoring tools based on the seagrass P. oceanica ecosystems, and discuss their strengths and weaknesses. This book tries to bring some light at this emerging applied field of the ecology, and should be especially useful to professionals in environmental studies, consulters and managers involved in the complex question of water quality assessment.