Behavior of sediment gravity flows can be influenced by seafloor topography associated with salt structures; this can modify the depositional architecture of deep-water sedimentary systems. Typically, salt-influenced deep-water successions are poorly imaged in seismic reflection data, and exhumed systems are rare, hence the detailed sedimentology and stratigraphic architecture of these systems remains poorly understood. The exhumed Triassic (Keuper) Bakio and Guernica salt bodies in the Basque–Cantabrian Basin, Spain, were active during deep-water sedimentation. The salt diapirs grew reactively, then passively, during the Aptian–Albian, and are flanked by deep-water carbonate (Aptian–earliest Albian Urgonian Group) and siliciclastic (middle Albian–Cenomanian Black Flysch Group) successions. The study compares the depositional systems in two salt-influenced minibasins, confined (Sollube basin) and partially confined (Jata basin) by actively growing salt diapirs, comparable to salt-influenced minibasins in the subsurface. The presence of a well-exposed halokinetic sequence, with progressive rotation of bedding, beds that pinch out towards topography, soft-sediment deformation, variable paleocurrents, and intercalated debrites indicate that salt grew during deposition. Overall, the Black Flysch Group coarsens and thickens upwards in response to regional axial progradation, which is modulated by laterally derived debrites from halokinetic slopes. The variation in type and number of debrites in the Sollube and Jata basins indicates that the basins had different tectonostratigraphic histories despite their proximity. In the Sollube basin, the routing systems were confined between the two salt structures, eventually depositing amalgamated sandstones in the basin axis. Different facies and architectures are observed in the Jata basin due to partial confinement. Exposed minibasins are individualized, and facies vary both spatially and temporally in agreement with observations from subsurface salt-influenced basins. Salt-related, active topography and the degree of confinement are shown to be important modifiers of depositional systems, resulting in facies variability, remobilization of deposits, and channelization of flows. The findings are directly applicable to the exploration and development of subsurface energy reservoirs in salt basins globally, enabling better prediction of depositional architecture in areas where seismic imaging is challenging.