Benthic foraminiferal assemblages in 24 sediment surface samples collected at water depths ranging from 9 to 103 m on the continental shelf off Guadiana River were analysed, leading to the identification of a total of 270 species. Cluster analyses performed on species with a relative abundance higher than 5% led to the identification of four assemblages. The shallowest assemblage, down to 12 m water depth, is represented by Ammonia beccarii, Asterigerinata mamila, Eggerelloides scaber, Mississipina concentrica, Planorbulina mediterranensis, Elphidium crispum and Quinqueloculina laevigata. A second assemblage between 12 and 40 m water depth is characterised by Bulimina elongata, Cribrononion gerthi and Nonion fabum. The assemblage between 40 and 95 m water depth is characterised by Bolivina dilatata, Epistominella vitrea, Bulimina aculeata, Bolivina ordinaria, Spiroloxostoma croarae and Nonionella iridea. Finally, below a depth of 95 m on the upper outer shelf, an assemblage exists characterised by Brizalina spathulata, Bulimina marginata, Cassidulina minuta, Brizalina subaenariensis, Cassidulina laevigata and Uvigerina peregrina. The spatial distribution of assemblages is closely associated with sea-bottom sedimentary environments and bathymetry. The number of benthic foraminiferal tests, and the distribution of several nearshore species within the two shallowest assemblages are clearly influenced by the outflow of the Guadiana Estuary and by local hydrodynamic conditions. The deeper water assemblages, on the other hand, were found to be more related to low levels of tidal energy, low oxygen environments associated to fine-grained sediments, and cold-water filaments related to seasonal upwelling.