Seagrasses are flowering plants that inhabit coastal and transitional waters. They colonize sedimentary seabeds (and to a lesser extent rocky substrates) and present unique adaptations to the marine environment. Seagrasses are especially sensitive to environmental deterioration and live in a world that is particularly threatened by human activity. The response of the plants and their associated communities to disturbances is relatively well known. This has facilitated the development of a large number of seagrass bioindicators based on biochemical, physiological, morphological, structural, demographic, and community measures, especially after the deployment of the EU Water Framework Directive (WFD) and to a lesser extent the implementation of the Marine Strategy Framework Directive. Bioindicators are at the interface between science and policy. In order for their use by managers for different purposes (monitoring, water quality assessment, long-term changes, etc.) to be robust and consistent, a clear definition of management goals is needed. The development of bioindicators must also be based on careful evaluation together with rigorous and transparent selection processes to ensure their scientific credibility. Here, we present bioindicator indices based on seagrasses that were developed with the context of the implementation of the WFD in Catalonia, NE Spain, to assess the ecological status of coastal and transitional water bodies. Ecological status includes aspects concerning both the quality of the biological community and the hydrological and chemical characteristics of the environment. For this reason, and to develop a WFD-compliant system for ecological status assessment based on Mediterranean seagrasses, we used multivariate techniques to combine different bioindicators, gathered from different levels within the biological organization, into single biotic indices (POMI and CYMOX, based on the species Posidonia oceanica and Cymodocea nodosa, respectively). We report how this was achieved and how the robustness and reliability of those indices were assessed through correlation with human pressures, uncertainty analysis, and intercalibration. Finally, besides their applicability, we discuss their shortcomings and what we, as seagrass biologists, have learned overall from responding to the challenges posed by the WFD and specifically by the part dealing with seagrasses.