The object of this study is magnesian clay minerals present in carbonate rocks of the post-rift phase of the pre-salt in the Santos Basin. These rocks developed in an Aptian-age alkaline lacustrine environment. This study summarizes the formation of clay minerals associated with different lithotypes in a range of 19 m and a depth of more than 5100 m. They were characterized from petrographic analysis by optical microscopy, X-ray diffraction (total sample and clay fraction), and modeling by Newmod®; and examined and analyzed by scanning electron microscopy. An approach based on identifying lithotypes and characterization of microsites allowed us to understand the occurrence of different clay minerals. Kerolite was the most abundant mineral in the sampled range. It occurs in lamellar aggregates under greater preservation of the original rock lamination and in association with spherulites and shrubs. The Stv/Ker mixed layers occurs in the same association, and formed finer unlaminated aggregates associated with the more intense dolomitization and silicification processes. Saponite occurs associated with detrital minerals forming clayey levels intercalated with microcrystalline carbonates. Fluids with a high Mg/Si and pH < 9 favor the precipitation of kerolite. The increase in pH during diagenesis may be responsible for the formation of Stv/Ker mixed layers.