For the first time during an Integrated Ocean Drilling Program (IODP) Expedition (Exp. 339, Mediterranean Outflow) water samples for living coccolithophore distributions and mudline samples for coccoliths, benthic foraminifera, and geochemical analyses in the underlying surface sediments were collected. In total, 14 water samples (from 5 to 20 m water depth) and 7 mudline samples were gathered at the drill sites. Coccolithophore distributions show spatial variations in species diversity. In particular, assemblages that characterize the Western Iberian Margin differ from those in the Gulf of Cadiz, indicative of oceanographic and environmental controls on the community in the upper ocean (0–20 m depth). Comparison of the living assemblages to those in surface sediments shows differences in the presence of some species, suggesting the influence of post deposition sedimentary processes. Other factors such as the season of sampling and the limited sampling depth may also have a role in the differences recorded. Benthic foraminiferal assemblages seem to be primarily determined by source, quantity and quality of available food. Sites in the Gulf of Cadiz are bathed by Mediterranean Outflow Water (MOW) and characterized by a considerable amount of advected food particles. Elevated epibenthic foraminifera exploit this niche, while arborescent epifaunal and infaunal taxa thrive on food particles falling out of MOW. The combined data suggest different flow speeds and settling of MOW suspension load in the Gulf of Cadiz. In contrast, assemblages from the Western Iberian Margin located farthest from or outside of MOW are determined by local export productivity and mirror trophic conditions in the surface waters. Both assemblages reveal variation in the composition at intermediate and deep water depths along the southern and western Iberian Margins with distance from the Strait of Gibraltar.