Present day submarine canyons are active conduits for large volumes of sediment, carbon, and pollutants from continents to oceans. However, the evolution of submarine canyons over geological timescales remains poorly understood due to their erosional nature and low preservation potential. The Late Cretaceous Punta Baja Formation represents a well-preserved submarine canyon-fill on a tectonically-active ocean-facing margin. Outcrops provide km-scale continuous strike and dip sections of the 120 m thick and 1.2 km wide feature. An inherited tectonic fabric influenced the location and orientation of canyon incision into fluvial bedrock. The stratigraphic evolution of the Punta Baja submarine canyon is reconstructed from incision to fill, and shows that it remained an active sediment conduit throughout the time period represented by the preserved fill. The depositional architecture of the north-south oriented erosionally confined canyon-fill is asymmetric, with sub-vertically stacked channel-fills to the west, and an overbank confined by the canyon margin in the east. Sedimentary process interactions led to depositional patterns that we consider distinct to submarine canyon fills. Dynamic topography created by mass wasting processes captured sediment and drove knickpoint development, an autogenic mechanism that modifies sediment delivery to the ocean floor. We interpret widespread upstream dipping surfaces in channel-fills as the stratigraphic expression of migrating supercritical-flow bedforms, playing an important role in sediment storage and transport in the canyon. The proximal location of canyons and unique confinement configuration impact transverse and lateral gravity flow filtering, causing depositional patterns in the intra-canyon overbank areas that are less well organised than in published examples of external levees and which were previously poorly characterised for submarine canyons. This study provides insight into how processes that are observed in modern canyons are selectively preserved through the lifetime of the canyon and construct or destroy stratigraphy on geological timescales.