In the Danube River Basin multiple pressures affect the river system as a consequence of river engineering works, altering both the river hydrodynamics and morphodynamics. The main objective of this paper is to identify the effects of hydropower development, flood protection and engineering works for navigation on the Danube and to examine specific impacts of these developments on sediment transport and river morphology. Whereas impoundments are characterised by deposition and an excess of sediment with remobilisation of fine sediments during severe floods, the remaining five free-flowing sections of the Danube are experiencing river bed erosion of the order of several centimetres per year. Besides the effect of interruption of the sediment continuum, river bed degradation is caused by an increase in the sediment transport capacity following an increase in slope, a reduction of river bed width due to canalisation, prohibition of bank erosion by riprap or regressive erosion following base level lowering by flood protection measures and sediment dredging. As a consequence, the groundwater table is lowered, side-arms are disconnected, instream structures are lost and habitat quality deteriorates affecting the ecological status of valuable floodplains. The lack of sediments, together with cutting off meanders, leads also to erosion of the bed of main arms in the Danube Delta and coastal erosion. This paper details the causes and effects of river engineering measures and hydromorphological changes for the Danube. It highlights the importance of adopting a basin-wide holistic approach to river management and demonstrates that past management in the basin has been characterised by a lack of integration. To-date insufficient attention has been paid to the wide-ranging impacts of river engineering works throughout the basin: from the basin headwaters to the Danube Delta, on the Black Sea coast. This highlights the importance of new initiatives that seek to advance knowledge exchange and knowledge transfer within the basin to reach the goal of integrated basin management.