The analysis of 17 cores collected in the Odiel Estuary (SW Spain) permits delimiting the recent evolution of this zone during the past decades and the influence of natural and anthropogenic factors on the distribution of Ostracoda and Foraminifera. In the upper estuary, the coincidence of acid waters, prolonged subaerial exposure, and coarse sediments may explain the absence or the disappearance of these microorganisms during the industrial period (1966-1985) in the major part of this area. In the lower estuary, sedimentary evolution and industrial wastes are the main factors influencing both the distribution and trends of the populations of these two groups. Finally, the main changes observed in the marine estuary are due to the sedimentary effects of the construction of two banks and the dredging of the main estuarine channel.