Sediment gravity flows have a propensity to infill lows and build depositional relief, which influences subsequent flows. This flow–deposit interaction is intrinsic to the evolution of submarine fans at a range of scales. A novel approach is presented that assesses the interaction of turbidity currents with a subtle but evolving depositional topography. Conceptual models developed from outcrop observations are tested with a process-based numerical model. The outcrop dataset was collected from submarine lobe deposits extensively exposed in the Tanqua depocenter, SW Karoo Basin, South Africa. The process-based numerical model of turbidity-current flow and sedimentation (FanBuilder) is used to mimic the process sedimentology. Input parameters of flows are constrained by observations of the outcrop geology (sedimentology and depositional architecture). Modeling results are analyzed and compared with outcrop observations and, where necessary, lead to iterative refinement of the underlying conceptual process-sedimentological model. The model successfully developed characteristic features of the depositional architecture, such as finger-like geometries and stacking patterns, which are comparable in scale and geometry to those observed in outcrop. The results highlight that lobe deposits have intricate geometries that, when stacked, form a complicated internal stratigraphy, in contrast to simple models of lobes consisting of laterally extensive sheets. In addition, new insights into the processes of lobe growth have come from the modeling that can be tested at outcrop in the future. Process modeling indicates that the stratigraphic complexity can be controlled by a subtle and dynamic depositional surface that drives instability in the position of distributive channels and the site of deposition. As such, this research emphasizes the importance of autogenic controls on the depositional architecture of submarine fan systems.