Anomalies in the frequency of river floods, i.e., flood-rich or -poor periods, cause biases in flood risk estimates and thus make climate adaptation measures less efficient. While observations have recently confirmed the presence of flood anomalies in Europe, their exact causes are not clear. Here we analyse streamflow and climate observations during 1960-2010 to show that shifts in flood generation processes contribute more to the occurrence of regional flood anomalies than changes in extreme rainfall. A shift from rain on dry soil to rain on wet soil events by 5% increased the frequency of flood-rich periods in the Atlantic region, and an opposite shift in the Mediterranean region increased the frequency of flood-poor periods, but will likely make singular extreme floods occur more often. Flood anomalies driven by changing flood generation processes in Europe may further intensify in a warming climate and should be considered in flood estimation and management.