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This study focuses on the foraminiferal distribution on intertidal mudflats of two contrasted estuaries (Auray and Vie) along the French Atlantic coast. In both estuaries, the foraminiferal communities are dominated by <i>Haynesina germanica</i> and the <i>Ammonia tepida</i> group. Stations located near the outlets show a high diversity and abundance of species of the genus <i>Elphidium</i>. Stations in the inner estuary show a higher proportion of agglutinated species (<i>Ammotium salsum</i>, <i>Ammobaculites agglutinans</i>). Multivariate statistical analysis suggests that the distance to the sea and the percentage of fine sediment (<63 µm) are the two main parameters explaining the foraminiferal distribution. Chemical analyses of the sediment show that the two studied estuaries are not affected by major anthropogenic pollution, so that the faunas should mainly reflect the natural controlling parameters. Three indices of environmental quality commonly used in coastal areas show counter-intuitive differences between stations, suggesting that these indices may be less reliable for use in intertidal estuarine mudflats. The newly developed Marine Influence Index (MII) integrates three major ecological factors: the position of the sampling point on the salinity gradient, the emergence time at low tide and the relative importance of fresh water discharge. In our dataset, MII shows significant correlations with the controlling environmental parameters (distance to the sea, percentage grains < 63 µm), as well as with the foraminiferal patterns (PCA axis 1, species richness, percentage of <i>Elphidium</i> spp. and <i>Quinqueloculina</i> spp.). These results suggest that the MII explains a substantial part of the faunal variability on estuarine intertidal mudflats, and can be used to detect deviations from the natural distribution patterns in response to anthropogenic pollution.