This study aims to provide a better understanding of the genesis and diagenetic evolution of the rift pre-salt deposits of the Santos Basin, in the context of evolution of the lake system in which the sediments were deposited. The study of the syngenetic and early diagenetic constituents and their paragenetic relations allowed reconstruction of the evolution of lacustrine environmental conditions during the rift stage in the central area of the basin. A petrological study was performed on cores and sidewall samples of a well drilled through the pre-salt rift section in the Lower Cretaceous of the central Santos Basin, eastern Brazilian coast. The studied rocks consist of carbonate and non-carbonate intrabasinal components, with extrabasinal non-carbonate contribution. During Barremian early rift sedimentation, intense syngenetic precipitation of magnesian clay minerals under highly alkaline conditions deposited arenites constituted by stevensite ooids and peloids, as well as hybrid, resedimented deposits of the Piçarras Formation. Freshening of the lacustrine environment provided the conditions required for the proliferation of bivalves and sedimentation of the coquinas of the Itapema Formation. The massive structure of the deposits, poor sorting, chaotic to concave-up orientation of the bioclasts, and mixing of bivalves with stevensite particles indicate redeposition by gravity flows. The main diagenetic processes in rift stevensite and hybrid rocks are the cementation and replacement of grains by calcite, dolomite, and subordinately, silica and smectite. Siliciclastic-volcaniclastic mudrocks present intense replacement by dolomite. In the bivalve rudstones, the main diagenetic processes were dissolution of the shells and cementation of the intraparticle and interparticle pores by calcite and, subordinately, dolomite and silica.