The influence of palaeodrainage characteristics, palaeogeography and tectonic setting are rarely considered as controls on stratigraphic organization in palaeovalley or incised valley systems. This study is an examination of the influence of source region vs. downstream base level controls on the sedimentary architecture of a set of bedrock-confined palaeovalleys developed along the distal margin of the Alpine foreland basin in south-eastern France. Three distinct facies associations are observed within the palaeovalley fills. Fluvial facies association A is mainly dominated by poorly sorted, highly disorganized, clast-to-matrix-supported cobble-to-boulder conglomerates that are interpreted as streamflood deposits. Facies association B comprises mainly yellow siltstones and is interpreted as recording deposition in an estuarine basin environment. Estuarine marine facies association C comprises interstratified estuarine siltstones and clean, well-sorted washover sandstones. The sedimentary characteristics of the valley fill successions are related to the proximity of depositional sites to sediment source areas. Palaeovalleys located proximal to structurally controlled basement palaeohighs are entirely dominated by coarse fluvial streamflood deposits. In contrast, distal palaeovalley segments, which are located several kilometres downstream, contain successions showing upward transition from coarse fluvial facies into estuarine central basin fines, and finally into estuarine-marginal marine facies. Facies distributions suggest that the fluvial deposits form wedge-shaped, downstream-thinning sediment bodies, whereas the estuarine deposits form an upstream-thinning wedge. The vertical stacking of fluvial to estuarine to marginal marine depositional environments records the fluvial aggradation and subsequent transgression of relatively small bedrock-confined river valleys, which drained a rugged, upland terrain. Facies geometries suggest that a fluvial sediment wedge initially prograded downvalley, in response to high bed load sediment yields. Subsequently, palaeovalleys became drowned during the passage of a marine transgression, with the establishment of estuarine conditions. Initial fluvial aggradation and subsequent marine flooding of the palaeovalleys is a consequence of the interaction of high local rates of sediment supply and relative sea-level rise driven by flexural subsidence of the basin.