Recent studies show that paleoenvironmental (allogenic) signals preserved in the stratigraphic record may be contaminated or overprinted by internally generated (autogenic) sedimentation. This is problematic, but it is unclear over what temporal and spatial scales autogenic patterns are most prevalent. We propose that scale breaks in basin-filling trends can be used to identify the transition between allogenic and autogenic stratigraphy. Using data from numerical and physical experiments and an ancient outcrop, we explore how compensation, the tendency for sediment transport systems to preferentially fill topographic lows, varies with stratigraphic scale. Object-based models demonstrate the temporal scales at which stratigraphy changes from being partially influenced by autogenic processes to being completely determined by allogenic forcings and suggest that this transition occurs at a time scale set by the maximum scale of surface roughness in a transport system divided by the long-term aggradation rate. This hypothesis is validated in a physical experiment where delta topography was monitored along flow-perpendicular transects at a high temporal resolution relative to channel kinematics. The strength of compensation in the experiment changes at the predicted time scale, where the maximum surface roughness is equal to the depth of the experimental channels. Above this compensation time scale deposits stack purely compensationally, but below this time scale deposits stack somewhere between randomly and deterministically. Similar scale-dependent stacking is also observed in the Ferris Formation (Cretaceous–Paleogene, Hanna Basin, Wyoming, United States). This study demonstrates that scale-dependent compensational stacking may be useful for isolating allogenic and autogenic stratigraphy in sedimentary basins.