A detailed pollen analysis has been carried out on two sediment cores taken from a marsh area located in the Doñana National Park, southwestern Spain. The studied sedimentary sequences contain a similar late Holocene record of vegetation and climate and show a progressive aridification trend since at least 5000 cal. yr BP, through a decrease in forest cover in this area. Long-term vegetation changes shown here (semi-desert expansion and Mediterranean forest decline) paralleled declining summer insolation. Decreasing summer insolation most likely impacted negatively on tree growing season as well as on winter precipitation in the area. Superimposed on the long-term aridification trend were multi-centennial scale periods characterized by forest reductions or increases in arid and halophytic plants that can be interpreted as produced by enhanced droughts and/or by local geodynamic processes. These are centered at ca. 4000, 3000–2500, and 1000 cal. yr BP, coinciding in timing and duration with well-known dry events in the western Mediterranean and other areas but could have also been generated by local sedimentary or geodynamic processes such as a marine transgression in a subsidence context and extreme wave events (EWEs). The alternation of persistent North Atlantic Oscillation modes probably played an important role in controlling these relatively humid–arid cycles.