Lagoons and marshes account for more than 50% of the coastal area in the Languedoc Roussillon region (South of France, Mediterranean Sea). The lagoons are very different in their physical and chemical characteristics, eutrophication level and resource exploitation mode. In this study, different levels of taxonomic diversity and two indices (D + and K + ) based on macrophyte, zoobenthos and fish communities are used to compare three lagoons (Ingril, Pre´vost and Mauguio). Whilst the taxonomic diversity of the fish community seems not influenced by the lagoon characteristics, the benthos community is strongly related to their eutrophication status. With the same sampling effort we identified 7 benthic species in Mauguio, the most impacted lagoon, while 24 species were found in the Ingril lagoon, which is the less impacted one. Overall, the variance of taxonomic distinctness K + appeared as the best indicator of the lagoon eutrophication level. This index is always highest for the Mauguio lagoon, whatever the biotic compartment considered. In a more stable environment like in the Ingril lagoon (lower variations of salinity, temperature or turbidity), K + is low, i.e., the structure of the taxonomic tree is very regular with a relatively homogeneous partition of species among phyla. By contrast, when salinity variations are wide, like in the Mauguio lagoon, the taxonomic tree becomes irregular with some lineages less constrained (many species belonging to the same family), while others are more impacted with a limited number of species in these phyla.