Abstract Regional and detailed seismic stratigraphic analyses of Early Cretaceous (Aptian) presalt carbonate sections from offshore Brazil reveal the complex stratigraphic architecture of late- and post-rift lacustrine carbonate systems. The lateral and vertical distribution of calibrated seismic facies within this framework highlights the evolution through time of the carbonate system and bathymetry of the host lacustrine basin. Despite the simple, largely abiotic and microbial components, lacustrine carbonate accumulations 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 reflects lateral variations in subsidence patterns combined with the interference of the basement topography, palaeowind directions and basinal filling patterns. Well-imaged clinoforms several hundred metres high attest to both the existence of significant lake-bottom topography, locally in excess of 800 m, and the occurrence of deep water at time of deposition. Platform margin trajectory and vertical and lateral architecture of clinoform packages through time reveal distinct sequence boundaries that can be correlated in detail only locally, demonstrating the impact of syndepositional tectonics, and possibly recurrent isolation of smaller lakes during lowstands. Depositional models from this study fill a gap in current understanding of lacustrine carbonate systems and offer a template for exploration and appraisal of the presalt play.