A multidisciplinary study from a number of drilled cores in the Guadalquivir estuary has made possible to identify as many as three extreme wave events and their facies in the 4th millennium BP (A: ~ 4000 cal yr BP, B: ~ 3550 cal yr BP, and C: ~ 3150 cal yr BP). These events, which caused strong erosion in the Guadalquivir sandy barrier and in the neighboring aeolian systems of El Abalario, brought about significant paleogeographical changes that may have affected human settlements established in the area during the Neolithic and Copper Age periods and during the Middle Bronze Age. The three events can be spatially correlated and their facies differentiated from more proximal to more distal from the coastline. The most proximal facies is characterized by a massive accumulation of shells, a sandy or sandy–muddy matrix, an erosive base, a highly diverse mixture of species (marine and estuarine), and lithoclasts. The most distal facies presents a muddy–sandy matrix, dominance of estuarine fauna, shell accumulation, presence of terrestrial species, mudpebbles, pebbles in a clayey matrix, and bioturbation. The evidence presented will further advance scientific knowledge about the impact of extreme wave events on coastal areas in SW Iberia and NW Africa.