Numerical models of formation of alluvial stratigraphy often specify, either explicitly or implicitly, the proportion of channel and overbank sediments that are deposited during a given interval of time. However, little is known about the factors that affect the partitioning of sediment between channels and the overbank environment over long time intervals, and the fidelity with which that partition is preserved in the stratigraphic record. Here we use physical experiments to investigate the role that discharge variability plays in this partitioning in fluvial stratigraphy. We find that channels formed under constant flow conditions have low lateral mobility and act mostly as conduits for sediments to reach the shoreline. The bulk of the aggradation in this case is derived from sediment-laden flow that escapes the main channels. By contrast, including floods increases channel lateral mobility, and this change is recorded in stratigraphy as an increased proportion of channel deposits relative to overbank deposits. When variable flow is included as an input condition a large volume of in-channel deposition occurs, rendering the channels substantial contributors to stratigraphic volume on their own. The increase in channel deposit volume is driven mainly by a threefold increase in the average time that a location is subject to in-channel aggradation. Other factors include a slight increase of in-channel aggradation rates, and an increase in erosion of the overbank environment that results from energetic overbank flows. Our study shows that the character of a river's hydrograph exerts a significant influence on the proportion of channel to overbank sediment bodies in alluvial successions, which is an unexamined source of uncertainty in common stratigraphic models.