The stable isotope composition of planktic and benthic foraminifera and the distribution of selected benthic foraminiferal species from a Messinian record of the lower Guadalquivir Basin, northeastern Atlantic Ocean, show that regional productivity changes were linked to glacioeustatic fluctuations. Glacial periods were characterized by poorly ventilated bottom waters as a result of weak Atlantic Meridional Overturning Circulation (AMOC), and by phases of high productivity related to intensified upwelling. In contrast, well-ventilated bottom waters owing to strong AMOC, the presence of degraded organic matter in the upper slope, and high input of degraded terrestrial organic matter derived from fluvial discharge to the outer shelf were recorded during interglacial periods. Before closure of the adjacent Guadalhorce Corridor at 6.18 Ma, which was the final active Betic Atlantic–Mediterranean gateway, the study area was alternately influenced by well-ventilated Mediterranean Outflow Water (MOW) and poorly ventilated Atlantic Upwelled Water (AUW). Following closure of the corridor, cessation of the MOW reduced the AMOC and promoted glacial conditions in the northern hemisphere, resulting in the establishment of local upwelling cells.