Empirical distribution functions of flood peaks in small catchments sometimes show discontinuities in the slope; that is, the largest flood peaks are significantly larger than the rest of the record. The aim of this paper is to understand whether these discontinuities, or step changes, can be a consistent effect of hydrological processes. We conducted field surveys in two Austrian alpine catchments 73 km² in size to map the spatial patterns of surface runoff generation and hydrogeologic storage. On the basis of this information, we selected the parameters of a distributed continuous runoff model, which is designed to simulate well the point when the storage capacity of the catchment is exhausted. Then we calibrated a stochastic rainfall model and performed Monte Carlo simulations of runoff to generate flood frequency curves for the two catchments. The curves exhibit a step change around a return period of 30 years. An analysis of the storage capacities suggests that this step change is due to a threshold of storage capacity being exceeded, which causes fast surface runoff in large parts of the catchments. The threshold occurs when the storage within the catchment is spatially rather uniform. To identify step changes, reliable estimates of the catchment storage capacity are needed on the basis of detailed hydrogeological information. The occurrence of a step change is of importance for estimating low-probability floods since the flood estimates with the step change accounted for can be significantly different from those based on commonly used distribution functions. We therefore suggest that step changes in the flood frequency curve of small catchments can be real and their possible presence should be taken into account in design flood estimation.