The Guadiana estuary (Iberian Peninsula, Europe) has low agriculture, industry and urban pressure, unlike other major Iberian estuaries; however, this situation is about to change. The Alqueva dam was constructed at 150 km from the river mouth, creating one of the biggest artificial lakes in Europe, which will support 110 000 ha of irrigation areas. Moreover, the estuarine margins are suffering increased human pressure. The risks that the Alqueva dam will pose to the downstream ecosystems, mainly to the estuary and adjacent coastal area, will be reviewed in this paper. Other issues are also analysed, as increased human desertification in the Portuguese basin, real estate pressure and the impact of the construction of a public infrastructure in the Portuguese lower estuary. Increased problems of sediment load reduction, water quality deterioration and shifts in the downstream fish populations are expected due to higher river flow reduction. Irreversible changes to estuarine margins and increased risk of pollution in the estuary will result from the multiple urban pressures. Lack of forest management and increased risk of wildfires, leading to water quality degradation and increased soil erosion, are a result of human desertification in the upper Portuguese basin. Multiple solutions to tackle these problems have to be considered. Creating the International Natural Park of the Lower Guadiana would not be enough and tourism should not be regarded as the only way to develop such a poor region. An ecohydrological approach of the basin should be implemented, to establish scientific based solutions to help solving conflicts and testing scenarios. Ultimately, the creation of a Portuguese-Spanish Basin Management Council for the lower Guadiana, involving those 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 produce ecological and sustainable management decisions.