The Guadiana River Estuary is located in the terminal part of a deeply incised river valley, which accumulated several tens of meters of sediments during the Holocenic transgression. Five cored boreholes (see Fig.1 for localisation) that reached the pre-Holocenic substratum were drilled recently in order to recognize the architecture of sedimentary facies and to quantify the accumulation of organic carbon trapped in sediments during the valley infilling by marine waters. It was assumed that due to structural constraints imposed by Palaeozoic and Mezozoic substratum, the main estuarine channel did not change its position significantly. Consequently borehole locations were chosen in order to represent different sedimentary environments in the estuary: proximity to the main channel (CM1 and CM3), external sea facing (CM4) and lagoonal (CM2 and CM5) environments.