AbstractThe distribution of biomarker compounds and magnetic susceptibility observed in the sediment from a 20 m core drilled in the marshlands of the estuarine region of the Guadalquivir River (southwest coast of Spain) has allowed us to reconstruct the palaeoenvironmental evolution of this area during the Holocene. Several organic compounds (n‐alkanes, n‐ketones, n‐alkanols, n‐alkanoic acids and organic sulphur), as well as different biomarker ratios, have been used to show changing environmental conditions through time. These geochemical proxies suggest good preservation of the organic matter, although some diagenesis has occurred to particular organic compounds, especially the n‐alkanoic acids. Our data indicate a major allochthonous supply of terrestrial plants, with less influence from aquatic plants or algae through the core. There are markedly different palaeoenvironmental conditions between the uppermost 5 m (last 6 ka cal. B.P.) and the rest of the core. From 5 m (ca 6 ka cal. B.P.) to 19 m (ca 8 ka cal. B.P.) depth the palaeoenvironmental conditions were almost constant. Based on organic sulphur content and n‐alkane content logs, anoxic conditions prevailed from 8 to 6 ka cal. B.P., while oxic conditions with enhanced convection of water (prevalence of fluvial input), and consequently a greater organic matter supply, predominated in the upper 5 m of the core. Similarly, little variation in the magnetic susceptibility profile below 5 m indicates stable environmental conditions, while in the upper 5 m conditions shifted to one with elevated water input and clastic sediment supply. This is linked to palaeofloral alterations in the Guadiamar/Guadalquivir drainage basins and/or anthropogenic effects. We propose that from ca 8 to 6 ka cal. B.P. a stable landscape physiognomy in the surroundings of the estuarine area of the Guadalquivir River, with a predominance of pines and grassland. However, over the last 6 ka cal. B.P. a variation in the terrestrial plant biomarker compounds suggests an alternation of relatively dry and humid phases and/or the impact of human populations on altering the vegetation community have occurred. Copyright © 2007 John Wiley & Sons, Ltd.