Abstract Regional and detailed seismic stratigraphic analyses of Early Cretaceous (Aptian) pre-salt carbonate sections in the offshore South Atlantic reveal the complex stratigraphic architecture of lacustrine carbonate systems that developed during late- and post-rift tectonic phases. The lateral and vertical distribution of calibrated seismic facies within this framework highlights the stratigraphic evolution of the pre-salt carbonate system. Despite the simple, largely abiotic and microbial components, lacustrine carbonates formed complex geometries that closely resemble those observed from marine systems, suggesting that a downward tapering carbonate production profile must have occurred. The complexity of the stratigraphic architecture in the presalt system reflects lateral variations in subsidence patterns combined with the interference of the basement rugosity, paleo-wind directions, and basinal filling patterns. Well-imaged clinoforms several hundred meters high attest to both the existence of significant lake-bottom topography and the at least occasional occurrence of deep water at time of deposition of the carbonate units, although rapid variations in base level are predicted. The shape of clinoforms varies from linear or tangential, have an average dip angle of 8–12° (depositional slopes) but can be up to 18–20° dip (bypass slopes), to erosional (>30° dip), reflecting differences in antecedent topography, and from tabular to climbing, reflecting varying rates of sediment accumulation in the basin. Closely spaced basement highs formed the nuclei for coalescing systems in the post-rift phase when subsidence rates where greatly subdued; margins abutting deep basins developed aggradational and retrogradational stacking patterns having erosional collapse scars and gravity flow deposits at the basin margin. Platform margin path and vertical and lateral architecture of clinoform packages through time reveal distinct sequence boundaries that can be correlated in detail only locally, demonstrating the large impact of syndepositional tectonics and possibly the recurrent isolation of smaller lakes during lowstands.