The three main estuaries in the French Atlantic coast – the Seine, Loire and Gironde, all with high tidal regimes – are interfaces between the continental and the coastal ecosystems. The Seine and Gironde are highly contaminated, whereas the Loire remains in a more natural state. Both the Seine and Gironde have suffered from harbour construction, and as a result, their biological units are extremely compartmentalized. Benthic species and communities have adapted to tolerate temporal physical and chemical changes (e.g. salinity, substrata, depth, and levels of fine particles and oxygen) and human activities (e.g. dredging, shipping traffic, and habitat reduction). Although numerous bio-indicators and indices are used to define the ecological quality status (EcoQS) of coastal waters, very few of them were developed specifically for environments with a mosaic of conditions and salinity levels, including freshwater. The main problem appears to be that all the indices for determining anthropogenic stress examine the abundances of stress-tolerant species, which may also be able to tolerate natural stressors such as those occurring in estuaries. This paper takes a look at the development status of the benthic indicators and index approaches used in the three main estuaries along the French Atlantic coast. In addition, it examines the adaptation of the different benthic indicators to the taxonomic sufficiency principle, and the adaptation of the Benthic Opportunistic Polychaetes Amphipods index (BOPA) and the Benthic Opportunistic Annelida Amphipod index (BO2A) for use in the freshwater zones of transitional waters (i.e. up to the upper limit of the tidal range). Several perspectives are discussed in light of the diverse disturbances and the heterogeneity of such stressed zones, such as the use of multimetric and scoring approaches.Read less <