The European Water Framework Directive (WFD) establishes a well differentiated typology of water bodies on the basis of scientific and biological criteria. For coastal waters, such criteria have long been established, while for transitional waters they are still under discussion. One of the difficulties when applying the WFD to coastal lagoons is to include them in only one of these categories, and while there is no doubt about the nature of estuaries as transitional waters, there is some controversy concerning lagoons. To what extent, reference conditions may be similar for estuaries and lagoons, or whether features common to all coastal lagoons are more important for differentiating them from other water bodies than the fact that there is (or is not) any fresh water influence, is something that remains unclear and is discussed in this work. Coastal lagoons and estuaries form part of a continuum between continental and marine aquatic ecosystems. Shelter, strong boundaries or gradients with adjacent ecosystems, anomalies in salinity regarding freshwater or marine ecosystems, shallowness, etc. all contribute to the high biological productivity of estuaries and lagoons and determine common ecological guilds in the species inhabiting them. On the other hand, fresh water influence, the spatial organization of gradients and environmental variability (longitudinal one-dimensional gradients in estuaries versus complex patterns and three-dimensional heterogeneity in lagoons) constitute the main differences, since these factors affect both the species composition and the dominance of certain ecological guilds and, probably, the system's complexity and homeostatic capability. In the context of the WFD, coastal lagoons and estuaries are closer to each other than they are to continental or marine waters, and, on the basis of the shared features, they could be intercalibrated and managed together. However, coastal lagoons cannot be considered transitional waters according to the present definition. To assume that fresh water influence is an inherent characteristic to these ecosystems could lead to important changes in the ecological organization and functioning of coastal lagoons where natural fresh water input is low or null. In our opinion, the present day definition of transitional waters should be changed substituting the criterion of fresh water influence by another based on common features, such as relative isolation and anomalies in salinity in water bodies with marine influence. Otherwise, coastal lagoons should be considered a particularly characteristic type of water mass for establishing reference conditions of ecological status.
