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Abstract Precipitation extremes will increase in a warming climate, but the response of flood magnitudes to heavier precipitation events is less clear. Historically, there is little evidence for systematic increases in flood magnitude despite observed increases in precipitation extremes. Here we investigate how flood magnitudes change in response to warming, using a large initial-condition ensemble of simulations with a single climate model, coupled to a hydrological model. The model chain was applied to historical (1961–2000) and warmer future (2060–2099) climate conditions for 78 watersheds in hydrological Bavaria, a region comprising the headwater catchments of the Inn, Danube and Main River, thus representing an area of expressed hydrological heterogeneity. For the majority of the catchments, we identify a ‘return interval threshold’ in the relationship between precipitation and flood increases: at return intervals above this threshold, further increases in extreme precipitation frequency and magnitude clearly yield increased flood magnitudes; below the threshold, flood magnitude is modulated by land surface processes. We suggest that this threshold behaviour can reconcile climatological and hydrological perspectives on changing flood risk in a warming climate.