In this study, living (Rose Bengal stained) foraminiferal faunas from 31 stations along the entire French Mediterranean Sea coast except Corsica have been analysed. In the context of the Water Framework Directive, the aim was to develop a biotic index to evaluate the benthic ecosystem quality. Therefore, different faunal parameters (diversity indices, wall structure proportion, and indicative species groups) have been tested to determine their relevance as indicators of environmental conditions. The best results are obtained with a biotic index based on the relative proportion of stress-tolerant taxa. For ecosystem quality evaluation, it is essential to distinguish between natural and anthropogenic eutrophication phenomena. In order to do so, we applied a correction on our biotic index, using the expected percentage of stress-tolerant species in natural environments, in function of sediment grain size (percentage <63 μm). Finally, a comparison of the different faunal parameters calculated for two different sediment intervals (0–1 and 0–4 cm) indicates clearly that the analysis of the uppermost centimetre of the sediment is sufficient to obtain relevant information needed for bio-monitoring purposes.