One hundred and three suprabenthic hauls in the Seine Estuary were taken on a marine to fresh water gradient with a modified Macer-GIROQ sledge during 1996 to collect Benthic Boundary Layer fauna. Two main species assemblages were identified along the salinity gradient: (1) a marine assemblage located in the downstream part of the estuary dominated by amphipods and mysids such as Schistomysis spp. and Gastrosaccus spp.; (2) an estuarine assemblage essentially dominated by the mysid Neomysis integer, recorded along the salinity gradient with maximal abundance observed between 15–10 psu. The decapod Palaemon longirostris and the goby Pomatoschistus microps were located in the upstream part of the estuary where they presented maximal abundances. Some species used the estuary during juvenile development such as the mysid Mesopodopsis slabberi (Van Beneden, 1861) and decapod Crangon crangon. Although the morphological characteristics of the Seine Estuary (weak estuarine area and important dredging) are different than other major European estuaries such as Gironde, Westerschelde and Ems, the longitudinal distribution of the demersal community presented similar patterns in all sites. Nevertheless, monthly sampling permitted to determine the seasonal location and abundance changes of the demersal assemblages in the Seine estuary. Marine assemblages presented maximal densities during summer and autumn while estuarine species were most abundant during spring and summer. Longitudinal changes of main demersal species during an annual cycle showed an increase of spatial distribution along the salinity gradient for marine and neritic species during spring and summer with a penetration of species in the estuary. The abundances of both assemblages were very high (annual mean >5000 ind 100 m−3) whereas the biomass of the estuarine assemblage was very important (annual mean ≅38 g ash-free dry weight 100 m−3).