European flood frequency and intensity change on a multidecadal scale. Floods were more frequent in the 19th (Central Europe) and early 20th century (Western Europe) than during the mid-20th century and again more frequent since the 1970s. The causes of this variability are not well understood and the relation to climate change is unclear. Palaeoclimate studies from the northern Alps suggest that past flood-rich periods coincided with cold periods. In contrast, some studies suggest that more floods might occur in a future, warming world. Here we reconcile the apparent contradiction by addressing and quantifying the contribution of atmospheric processes to multidecadal flood variability. For this, we use long series of annual peak streamflow, daily weather data, reanalyses, and reconstructions. We show that both changes in atmospheric circulation and moisture content affected multidecadal changes of annual peak streamflow in Central and Western Europe over the past two centuries. We find that during the 19th and early 20th century, atmospheric circulation changes led to high peak values of moisture flux convergence. The circulation was more conducive to strong and long-lasting precipitation events than in the mid-20th century. These changes are also partly reflected in the seasonal mean circulation and reproduced in atmospheric model simulations, pointing to a possible role of oceanic variability. For the period after 1980, increasing moisture content in a warming atmosphere led to extremely high moisture flux convergence. Thus, the main atmospheric driver of flood variability changed from atmospheric circulation variability to water vapour increase.