The European Water Framework Directive (WFD, 60EC, 2000) requires that a typology be developed at national and European level for the differentiation of ecologically distinct types within water categories. Although common typological descriptors have been defined for stream, lake and coastal areas, a typology for transitional waters has not yet been defined, and its implementation by the European countries is still under development. A set of 30 coastal lagoons from the Balearic archipelago were selected to act as case studies for the application of the WFD in the Mediterranean ecoregion. Within these systems, and according to normative definitions, we studied both biological (i.e., invertebrate and phytoplankton communities) and physico-chemical quality elements. Our objective is to propose an adequate typology for small Mediterranean coastal lagoons and to establish those criteria that, based on human pressures in the neighbouring perimeters, may allow the establishment of type-specific reference conditions. The salinity range was the only factor that enables to differentiate, in a first phase of application, ecologically relevant typologies in the studied Mediterranean islands. Other descriptors, such as tidal range and geographic localisation of the studied area had scarce relevance. The analysis of the data suggests a three-level typology for the Mediterranean coastal lagoons: oligohaline (up to 5 of salinity); mesohaline (6-26) and euhaline (>26). A total of 6 out of the 30 studied lagoons fulfil the reference criteria, covering the three salinity types proposed. The invertebrate communities showed a consistent agreement with the proposed typology, while the phytoplankton did not. Moreover, the inherent variation in the biological communities across salinity types was higher than that obtained when a subtypology based on the annual salinity range of each lagoonwas applied. These results support the need for further research on the ecology of small coastal lagoons, focused on the applied aspects addressing scientific and technical implementation of WFD at the national and European levels.