Here we show how a continuum granular flow model can replicate realistic self-organizing subaqueous bedforms, and we explore how a record of this dynamic topography is transferred into the substrate where it can be fossilized. Modeled bedform behavior is quantitatively compared to laboratory and field data. Sediment scouring and deposition by migrating bedforms produce sets of partially preserved bedforms recording nonlinear behavior at the sediment-fluid interface. Model results show the importance of spatial and temporal variations in bedform size and migration rate to the generation of sets. Addition of net bed aggradation to modeled bedforms allows us to explore the preservation of topography under a wide range of depositional conditions. We present new relationships among aggradation rate, bedform migration rate, and set thickness. Variability of set thickness is shown to be a product of the competition between bed aggradation and bedform migration rates. These results show how using the entire distribution of set thickness for ancient strata can refine estimates of the formative paleoenvironmental conditions.