ABSTRACTAutogenic feedbacks can produce large‐scale, organized stratigraphic patterns in alluvial fans, but autogenic depositional signatures of specific upstream boundary conditions remain challenging to interpret. Here, a combination of theory, experiment and field application is used to explore how autogenic lithofacies changes can be interpreted as stratigraphic indicators of upstream boundary conditions. Six experiments were conducted to test the effects of sediment supply and water discharge rates on autogenic advance and retreat of the lithofacies boundary (grain‐size transition) in an alluvial fan with two dominant grain sizes. Migration of the grain‐size transition caused a short‐term zigzag pattern in the grain‐size transition position in the dip‐directional deposit section. For each experiment, time‐lapse images and laser topographic scans of the fan surface and stratigraphic cross‐sections of the final deposits were used to quantify characteristic timescales of autogenic processes. Timescales for fan‐margin migration, surface wet‐fraction change and grain‐size transition migration generally shorten as sediment supply rate increases and water discharge rate decreases. Increasing the sediment supply rate shortens the duration of the fluvial sediment storage and release cycle, producing higher frequency zigzags in the grain‐size transition trajectory. Increasing the water discharge tends to widen channels and lengthens the duration of the fluvial sediment storage and release cycle, constructing lower frequency zigzags in the grain‐size transition trajectory. Increasing the water discharge also enables more sediment to transport further downstream during release events, leading to higher magnitude zigzags in the grain‐size transition trajectory. These relationships between upstream boundary conditions and the grain‐size transition trajectory demonstrate how autogenic stratigraphic signals could be used as a tool to infer relative changes in boundary conditions.