Lagoons are highly productive areas representing more than 50% of the coastline area in Languedoc-Roussillon (South of France, Mediterranean sea). These lagoons are very different in their environmental conditions, human influences, eutrophication levels and aquaculture intensity. Based on macrophyte communities associated with soft substrates, two indices of taxonomic diversity (the “average taxonomic distinctness” (Δ⁺) and the “variation in taxonomic distinctness” (Λ⁺)) were used to discriminate four of these lagoons (Thau, Salse-Leucate, Bages-Sigean and Mauguio). Bages-Sigean presented a significant higher average taxonomic distinctness (p<0.05) and Salse-Leucate had a significant higher variation in taxonomic distinctness (p<0.05) without considering exotic species. The index values were neither influenced by sample size nor by presence of exotic species. Thus, the “average taxonomic distinctness” was related to human activities and eutrophication level whereas the “variation in taxonomic distinctness” was more related the environmental variability, associated with the prime stressor of salinity in brackish coastal lagoons.