This paper refers to the effects of projected water transfers, envisaged in the Spanish National Hydrological Plan, on the ecology of the lower River Ebro and its delta. Present management strategies, have resulted in highly eutrophic river water and a salt wedge which runs for more than 30 km upstream from the river mouth and its presence has been recorded during most of the year. Some parts of the delta coast are in regression as most of the inorganic sediments carried by the river are trapped in the dams. This is also leading to the sinking of the deltaic plain because subsidence and eustatic sea level rise are not compensated by new sediments. The high productivity of two bays and the coastal zone adjacent to the delta is related to influx of freshwater from irrigation channels, used in rice cultivation and the river. In the new National Hydrological Plan, a withdrawal of water upstream from the delta of 2012 hm3/year (15% of the mean annual discharge) is planned as well as the construction of 49 new reservoirs, mainly for irrigation purposes. A minimum river flow of 100 m3/s will be established by the Plan. If the plan is carried through, due to the water abstraction, forecasts based on ecological studies in the area predict: (1) increased presence of the salt wedge in the final 18 km of the river with detrimental effects on river fauna and flora; (2) serious threats to aquaculture and fisheries in the bays; (3) reduction of fish and crayfish production in the platform area; (4) further reductions in sediment and freshwater inputs to delta; (5) salinization of fields under cultivation; and (6) detrimental side effects on deltaic ecosystems.