In a 10-stations bathymetrical transect in the Bay of Biscay, we observed important changes in the density, composition and microhabitats of live foraminiferal faunas from the outer continental shelf to the abyssal plain. Four zones are recognised: (1) at the upper continental shelf (140 m water depth), foraminiferal densities are very high and the superficial sediment is occupied by Bolivina subaenariensis and Valvulineria bradyana. Globobulimina spp., Chilostomella oolina and Nonion fabum dominate the infaunal niches, which are positioned close to the sediment–water interface due to a strong compaction of the vertical succession of redox zones. (2) At the upper continental slope stations (300–1000 m), foraminiferal densities are high and the superficial sediments are dominated by Uvigerina mediterranea/peregrina. Deeper in the sediment, intermediate infaunal niches are occupied by Melonis barleeanus. Due to a deeper oxygen penetration, the deep infaunal taxa Globobulimina spp. and C. oolina live at a considerable depth in the sediment. (3) At the mid and lower slope stations (1000–2000 m) in the superficial sediment Cibicidoides kullenbergi and Hoeglundina elegans progressively replace U. mediterranea. U. peregrina is still a dominant taxon, reflecting its preference for a somewhat intermediate organic flux level. Deep infaunal taxa become increasingly rare. (4) At the lower slope and abyssal plane stations (deeper than 2000 m), faunal densities are very low and the fauna is composed exclusively by shallow infaunal species, such as Nuttallides umboniferus and Melonis pompilioides. The foraminiferal data together with the pore water data in the sediment give evidence of the presence of a trophic gradient from very eutrophic settings at the upper continental shelf towards oligotrophic settings at the abyssal area.