We used the individual-based multidimensional functional diversity and the taxonomic approaches in a complementary way to describe phytoplankton communities in three coastal lagoons with different eutrophication status in the South of France. We sampled communities during three seasons, i.e., in autumn, spring, and summer. Using classical taxonomy, 107 taxa/morphotypes were identified in the nine communities. The individual-based functional approach allowed grouping these individuals into 20 functional entities according to their values for 5 traits related to trophic adaptations (cell size, mobility, trophic regime, coloniality, and pelagic/benthic life). Some species (e.g., Prorocentrum micans) emerged in multiple functional entities, showing the importance to consider intraspecific variability. The functional description of phytoplankton communities better reflected the hydrological functioning and the different eutrophication status of the lagoons than the taxonomic approach. Specific functional adaptations were identified in the nine communities. For example, phytoplankton organisms with heterotrophic and potentially mixotrophic abilities occurred when the availability of inorganic nutrient decreased, or when organic matter and small preys were potentially the main nutrient resources. The limitation has also favored small cells highly competitive for nutrients. Using functional indices together with taxonomic description has also helped revealing important aspects of community assembly, such as competitive exclusion in summer.