Presalt lacustrine carbonate rocks forming highly productive Santos Basin discoveries below Aptian evaporites are described and interpreted here. Based on rock calibration to well logs and seismic data, the primary reservoir facies are Barremian–Aptian coquinas overlain by Aptian microbialites. Coquinas deposited primarily on rift highs are laterally surrounded by finer, organic-rich facies that accumulated during rift-interval, extensional faulting. Aptian microbial laminites, spherulitites, and shrubby boundstones (stromatolites) accumulated during sag-interval, flexural subsidence. The microbial influence, rather than exclusively abiotic processes, during the deposition of these facies has been deduced from the presence of fossilized, extracellular, polymeric substances in laminites, shrubs, and the micritic nuclei of spherulites; additionally, isotopic data are compatible with an organic, bioinduced origin. The interpreted depositional architecture and paleogeography comprise ramps, platforms, and buildups, measuring tens of meters in thickness and several kilometers laterally but with marked variations in reservoir facies. Reworked facies predominate on ramps, whereas buildups, located in areas with high rates of accommodation bordering the carbonate platform, are mostly stromatolites intercalated with reworked facies. No single depositional model captures the facies variability within this depositional system. Tectonics governed the system, basically controlling the accommodation space, the change over time from a freshwater rift lake to an alkaline and then saline sag lake conditioning a remarkable change in sedimentation pattern. In conclusion, physical processes controlled sedimentation of coquinas filling the accommodation on relative lows, whereas the microbial carbonates were ecologically controlled as demonstrated by the widespread organomineralization, and the distinct stacking patterns were dependent on the paleomorphology.