The Guadiana estuary (Iberian Peninsula, Europe) has low agriculture, industry and urban pressure, unlike other major Iberianestuaries; however, this situation is about to change. The Alqueva dam was constructed at 150 km from the river mouth, creatingone of the biggest artificial lakes in Europe, which will support 110 000 ha of irrigation areas. Moreover, the estuarine marginsare suffering increased human pressure. The risks that the Alqueva dam will pose to the downstream ecosystems, mainly to theestuary and adjacent coastal area, will be reviewed in this paper. Other issues are also analysed, as increased humandesertification in the Portuguese basin, real estate pressure and the impact of the construction of a public infrastructure in thePortuguese lower estuary. Increased problems of sediment load reduction, water quality deterioration and shifts in thedownstream fish populations are expected due to higher river flow reduction. Irreversible changes to estuarine margins andincreased risk of pollution in the estuary will result from the multiple urban pressures. Lack of forest management and increasedrisk of wildfires, leading to water quality degradation and increased soil erosion, are a result of human desertification in the upperPortuguese basin. Multiple solutions to tackle these problems have to be considered. Creating the International Natural Park ofthe Lower Guadiana would not be enough and tourism should not be regarded as the only way to develop such a poor region. Anecohydrological approach of the basin should be implemented, to establish scientific based solutions to help solving conflicts andtesting scenarios. Ultimately, the creation of a Portuguese-Spanish Basin Management Council for the lower Guadiana, involvingthose that are interested in the sustainable development of the Guadiana (local populations and associations, private stakeholders(dam managers, tourism entrepreneurs, farmers), local and national authorities, ENGO’s and scientists) is essential to produceecological and sustainable management decisions.