Reduction in channel capacity can trigger an increase in flood hazard over time. It represents a geomorphic driver that competes against its hydrologic counterpart where streamflow decreases. We show that this situation arose in the Guadalquivir River (Southern Spain) after impoundment. We identify the physical parameters that raised flood hazard in the period 1997–2013 with respect to past years 1910–1996 and quantify their effects by accounting for temporal trends in both streamflow and channel capacity. First, we collect historical hydrological data to lengthen records of extreme flooding events since 1910. Next, inundated areas and grade lines across a 70 km stretch of up to 2 km wide floodplain are delimited from Landsat and TerraSAR-X satellite images of the most recent floods (2009–2013). Flooded areas are also computed using standard two-dimensional Saint-Venant equations. Simulated stages are verified locally and across the whole domain with collected hydrological data and satellite images, respectively. The thoughtful analysis of flooding and geomorphic dynamics over multi-decadal timescales illustrates that non-stationary channel adaptation to river impoundment decreased channel capacity and increased flood hazard. Previous to channel squeezing and pre-vegetation encroachment, river discharges as high as 1450 m3·s−1 (the year 1924) were required to inundate the same areas as the 790 m3·s−1 streamflow for recent floods (the year 2010). We conclude that future projections of one-in-a-century river floods need to include geomorphic drivers as they compete with the reduction of peak discharges under the current climate change scenario.