On 18 June 2013, a damaging flood of the Garona River (Val d'Aran, Central Pyrenees, Spain) caused losses exceeding EUR 100 million. Few studies have related flood events to the geologic, tectonic and geomorphologic context. This study deals with both short- and long-term processes by studying the upper reach of the Garona River on different timescales and space scales. There has been a clear entrenchment tendency of the drainage network since the Miocene. Post-orogenic exhumation and uplift of the Axial Pyrenees determines the recent and active tectonics of the area and leads to fluvial incision. The last Upper Pleistocene glaciation affected Val d'Aran and gave rise to a destabilization period during the glacial-interglacial transition, marked by a postglacial incision tendency. Mean entrenchment rates between 0.68 and 1.56 mm yr−1 since deglaciation have been estimated. The assessment of the 2013 flood, characterized by the predominance of vertical incision and bank erosion, suggests that the long-term tendency of the fluvial system is reflected in short-term processes. The study of the geologic and geomorphologic evolution, combined with the analysis of this 30-50-year return period flood event, helps to improve flood risk management by providing contextual information that can constrain predictions and help guide choices and decisions. In fact, the millennial entrenchment tendency is shown at the human scale, which is considered useful for river management, but could be imperceptible in detailed hydrodynamic and channel morphology studies that describe river dynamics mostly at the 10-15-year timescale.