Seafloor topography affects the sediment gravity flows that interact with it. Understanding this interaction is critical for accurate predictions of sediment distribution, paleogeography, and structural reconstructions of deep-water basins. The effects of seafloor topography can be seen from the bed scale, through facies transitions toward intra-basinal slopes, to the basin scale, where onlap patterns reveal the spatial evolution of deep-water systems. Basin-margin onlap patterns are typically attributed to allogenic factors, such as sediment supply signals or subsidence rates, with few studies emphasizing the importance of predictable spatio-temporal autogenic flow evolution. This study aims to assess the autogenic controls on onlap by documenting onlap styles in the confined Eocene-to-Oligocene deep-marine Annot Basin of SE France. Measured sections, coupled with architectural observations, mapping, and paleogeographical interpretations, are used to categorize onlap styles and place them within a generic stratigraphic model. These observations are compared with a simple numerical model. The integrated stratigraphic model predicts that during progradation of a deep-water system into a confined basin successive onlap terminations will be partially controlled by the effect of increasing flow concentration. Initially thin-bedded low-density turbidites of the distal lobe fringe are deposited and drape basinal topography. As the system progrades these beds become overlain by hybrid beds and other deposits of higher-concentration flows developed in the proximal lobe fringe. This transition is therefore marked by intra-formational onlap against the underlying and lower-concentration lobe fringe that drapes the topography. Continued progradation results in deposition of lower-concentration deposits in the lobe off-axis, resulting in either further intra-formational onlap against the lobe fringe or onlap directly against the hemipelagic basin margin. Basinal relief is gradually reduced as axial and higher-volume flows become more prevalent during progradation, causing the basin to become a bypass zone for sediment routed down-dip. This study presents an autogenic mechanism for generating complex onlap trends without the need to invoke allogenic processes. This has implications for sequence-stratigraphic interpretations, basin subsidence history, and forward modeling of confined deep-water basins.