Recent excavations, under direction of the German Archaeological Institute Madrid, revealed extensive remains of Phoenician culture in the environs of the west-Andalusian city of Ayamonte, located at the mouth of the Guadiana River. Among others Phoenician tombs and the associated settlement were brought to light and provide information about the cultural landscape of the lowermost part of the Guadiana River around 3000 years ago. The Guadiana River is one of the major streams draining the Iberian Peninsula and its lower estuary has been extensively studied in terms of ecological stress due to damming (e.g. the Alqueva dam) and postglacial sea-level rise, but geoarchaeological studies are rarely found. This study aims to answer geoarchaeological questions arising during intensive discussions about landscape sensitivity and human-environment interactions in the surrounding of the mentioned excavations. Geomorphological and sedimentological investigations are coupled with archaeological information. Three selected landscape types with different research questions are presented in the form of detailed case studies: (a) the surroundings of the silted-up lagoonal-like environment of the “Estero de la Nao”, (b) the terrestrial archives of adjacent slopes, close to the excavation and (c) the coastal marshland of the lower Guadiana Estuary. The case studies reveal approximately 6000 years of rapid landscape change within the estuary and its environs. (a) The sedimentary archive of the lagoonal-like environment shows three important aspects of landscape development: (I) rapid siltation of a former open-water body, (II) indications on dredging activity in order to maintain an assumed anchorage in operation and (III) sedimentological traces of the tsunami generated from the Great Lisbon Earthquake in 1755. (b) Sedimentological results from adjacent slopes confirm early settlement activity with a long-standing erosive history, accounted geomorphic phases of slope stability and slope instability as well as evidence of early ore mining activity. (c) Sedimentological and cartographic studies of the estuarine marshland reveal a rapid coastal evolution, allowing to design a paleogeographic scenario of the Late Holocene development of the lower Guadiana Estuary.