Hydrodynamics, salinity intrusion and stratification in the Guadiana estuary were characterized using two- and three-dimensional models for fresh water flows covering the range of monthly averaged river flows for dry to wet years. Two- and three-dimensional circulation model results were then used to investigate the flushing properties of the lower estuary for passive organisms and for organisms with vertical migration capabilities, respectively. Stratification can occur in the Guadiana estuary for river flows as small as 10 m3 s−1, depending on the tidal amplitude. For homogeneous or weakly stratified conditions, salinity can be found upstream of Alcoutim (km 40) during neap tides, and extends even further for spring tides. For a river flow of 10 m3 s−1, euhaline conditions reach 25 km upstream of the mouth during spring tides. For larger river flows, the region under stratified conditions is located in the downstream 10 km, and its extent depends mainly on the tidal phase. For river flows between 50 and 300 m3 s−1, salinity intrusion does not extend beyond km 20. As the river flow increases, the upper limits of the several haline regions approach one another, creating a lower estuary where salinity conditions have a wide range of horizontal variability. Residence times of passive organisms in the lower Guadiana estuary depend on the magnitude of the river flow, tides and other mechanisms, varying from a few hours to 60 days in the range of river flows considered. The variability of residence times with different environmental conditions is similar for all river flows, the upper limit of residence times being about one order of magnitude larger than the lower limit. For river flows above 200 m3 s−1, both limits of residence times are small (from a few hours to a few days), showing the dominant role of river flow in these conditions. However, active organisms, with vertical migration capabilities, can remain inside the Guadiana estuary under strong river flows, by taking advantage of the phase lag along the vertical profiles of velocity under stratified conditions. Permanence conditions improve for organisms located in the main channel, due to the larger stratification in deeper areas. The tidal amplitude also plays an important role, spring tides being more favourable to permanence than neap tides.