Given the sparseness of geological data and the temporal scales at which fluvial systems operate (on a basin scale), how can we constrain variables such as climatically and tectonically controlled changes in sediment supply, water supply, subsidence, uplift, and sea level independently when trying to reconstruct paleo-environments and understand present day landscape dynamics? Here we examine example cases of an experimental sedimentary basin’s response to externally imposed change in these variables. First, we use a simple coordinate transformation that maps downstream distance in a fluvial system into the fraction of sediment supply deposited to that point. We found that analysis of fluvial stratigraphy in this framework clarifies both the effect of mass-balance changes as well as the residual effect of changes in other variables such as channel size associated with fluctuations in water supply (our experimental analogue to climate). Second, we demonstrate the limitations to using incised valleys to reconstruct paleoclimate and tectonic change. We show that autogenic fluvial processes can produce complex landscapes and stratigraphy that does not necessarily reflect allogenic forcing on the system, i.e. discrete changes in eustatic sea level, tectonics, or climate. We also demonstrate that valleys preserved in stratigraphy can be quite different in form from any topographic valley that ever existed during the interval in which the valley was evolving, therefore making paleoclimate interpretations from incised valley geometries difficult, if not impossible.