Although benthic macrophytes must be considered in monitoring programs to establish the ecological status of transitional and coastal waters in the European Union, the patterns of variability in species composition of macrophyte assemblages in Mediterranean coastal lagoons has scarcely been studied. In this work the spatial (both vertical and horizontal) and seasonal dynamics of macrophyte assemblages in a coastal lagoon (Mar Menor) are compared with those of open coastal assemblages in the SW Mediterranean to analyze any biological variability in lagoon assemblages and the factors that determine such variability. Different assemblages, characterized by well defined groups of species, can be described according to their isolation from the open sea and the type of substratum; at the same time, a vertical zonation pattern, similar to that found in all marine communities but more compressed, exists. This implies that when applying the EU Water Framework Directive or assessing environmental impact, a lagoon should not be considered spatially uniform and unique unit but as a mosaic of assemblages.