Short-term autogenic processes are thought to be averaged out by long-term allogenic forcing and have often been ruled out in stratigraphic interpretation. It is generally difficult to resolve the scale of autogenic effects on landscape evolution and even more so on sedimentary records. Here we analyze short-term variation in migration rate of the alluvial-bedrock transition in a series of experiments. The experiments developed a fan delta over a stationary, sloped, nonerodible basement with constant water and sediment discharges. The rate of base-level change varies between experiments but was constant for a given experiment. The location of the alluvial-bedrock transition varied autogenically in all experiments. The instantaneous migration rate of the alluvial-bedrock transition varied by as much as an order of magnitude more than that induced by allogenic forcing. The strong autogenic pulses can be explained by sediment storage and release due to intrinsic variation in the transport efficiency of the fluvial system. Data from experiments with base-level change indicate that the autogenic signal in the migrating alluvial-bedrock transition is weakest during landward migration (onlap), when base-level rises, and strongest during basinward migration (valley incision), when base-level falls. We use a one-dimensional geometric model to explain the variations in the autogenic response of the alluvial-bedrock transition as a function of direction of base-level change. The model periodically changes fluvial slope to represent the effects of sediment storage and release with base-level rise and fall. The modeling result reproduces the observed pattern of autogenic variation in alluvial-bedrock transition.