The distribution of channel deposits in alluvial basins is commonly used to interpret past changes in climate, tectonics, and sea level. Here we present preliminary evidence that long-time scale (∼103–105 yr) self-organization in fluvial systems may generate structured stratigraphic patterns spontaneously, in the absence of, or independent from, changing basin boundary conditions. A physical experiment and an ancient alluvial succession (Ferris Formation, latest Cretaceous–Paleogene, south-central Wyoming) both show stratigraphy where clusters of many closely spaced channel deposits are separated from each other by extensive intervals of overbank mudstones. Analysis using spatial point process methods shows that channel deposits in both basins are statistically clustered over intermediate basin length scales. In the experiment, external controls (base level, subsidence rate, and sediment/water supplies) were not varied, and therefore not factors in cluster formation. Likewise, the ancient system lacks stratigraphic and sedimentologic evidence of external controls on channel clustering. We propose that channel clusters, as seen in this study, reflect a scale of fluvial self-organization that is not usually recognized in ancient deposits. This type of internally generated stratigraphy should be considered when reconstructing tectonic, climate, and sea-level changes from ancient basin fills and when correlating between outcrop belts or subsurface wells.