This work reports the first description of benthic foraminiferal assemblages in the Gironde estuary (France) with a particular emphasis on the non-indigenous species Ammonia confertitesta. Four stations along the salinity gradient were monthly sampled for sediment and faunal parameters from September 2018 to December 2019. Ammonia confertitesta, Haynesina germanica, Ammonia aberdoveyensis, Ammonia veneta and Elphidium oceanense were the main species occurring at the four sampled stations. The distributions of the main foraminifera species in the Gironde estuary were majorly driven by the distance to the sea and sediment surface-chlorophyll-a. Total Organic Carbon, Total Nitrogen and Carbon:Nitrogen ratio had a minor influence. This study is the first to describe ecological preferences of the three congeneric Ammonia species, still often generically pooled as A. tepida in the literature, by discriminating them using a stereomicroscope. The non-indigenous species A. confertitesta, noticeably outcompetes the indigenous foraminiferal species along the whole estuary. The presence of the commercial harbour of Bordeaux in the Gironde estuary suggests that it may have been introduced by mean of ballast waters. High abundances compared to those of other indigenous Ammonia species found in the Gironde estuary may also suggest that A. confertitesta has a real potential of invasiveness when environmental conditions are suitable.